The leader of India's main opposition Bharatiya Janata Party (BJP), LK Advani, has submitted his resignation.
Mr Advani after laying a wreath at Jinnah's mausoleum
He offered to step down as party president at the end of a six-day visit to Pakistan, where he praised the nation's founder Mohammed Ali Jinnah.
But his description of Mr Jinnah as a "secular" leader created huge controversy back in India.
Mr Jinnah is still widely blamed for the partition of India because of his drive for a Muslim homeland.
The BBC's Nick Bryant in Delhi says that Mr Advani's trip to Pakistan was seen as an attempt to reposition himself politically, to cast off his hawk's clothing and recast himself as a moderate, more palatable to a wider electorate.
Mr Advani spoke of Mr Jinnah's "forceful espousal of a secular state in which every citizen would be free to practice his own religion".
He described the founder of Pakistan as one of the "very few who actually create history".
Hindu nationalist groups close to the BJP and the ruling Congress party have led the protests against his comments during his Pakistan visit.
But Mr Advani is standing by his comments.
"I have not said or done anything in Pakistan which I need to retract or review", Mr Advani wrote in a letter to a senior party member requesting the BJP to "relieve" him of the post of party leader.
"I believe that my visit to Pakistan last week has immensely reinforced the initiatives taken by the NDA (the previous BJP-led government) to bring about peace and normalcy in Pakistan," he said.
Mr Advani is considered one of the more hawkish members of the Hindu nationalist BJP. He could still face criminal charges for his role in the destruction of a mosque in the northern city of Ayodhya by a mob in 1992.
His statements in Pakistan, therefore, took many in Pakistan and India by surprise.
Mr Advani met Pakistan's prime minister in Islamabad
The BBC's Soutik Biswas in Delhi says that Mr Advani's description of Mr Jinnah had left him isolated within the BJP and Hindu nationalist pressure groups as they regard the founder of Pakistan as the architect of the partition of India on communal lines.
Hindu nationalist groups like the Rashtriya Shyamsevak Sangh (RSS) and the Vishwa Hindu Parishad demanded to know why Mr Advani had "heaped praise" on Mr Jinnah.
The RSS, the ideological fountainhead of various Hindu groups including the BJP, also protested against Mr Advani's statement that the day when the Babri mosque was destroyed in the northern Indian city of Ayodhya was the "saddest" in his life.
Mr Advani furthered angered the hardline Hindu groups when he told a meeting in Pakistan that the emergence of India and Pakistan as "two separate, sovereign and independent nations is an unalterable reality of history".
Many Hindu groups like RSS are still opposed to the idea of partition and talk about a "united India" comprising Pakistan and Bangladesh" in their maps and literature.
Mr Advani has also drawn criticism from India's governing Congress party.
"It is truly ironic and astounding that Mr Advani considers Mr Jinnah secular. Perhaps he would like to explain to the nation the new definition of secularism," Congress spokesman Abhishek Singhvi told the media.
Mr Advani was appointed president of BJP last October after the party suffered an electoral defeat in the western state of Maharashtra.
In Pakistan Mr Advani's remarks on Mr Jinnah aroused little interest.
However, the BBC's Aamer Ahmed Khan in Karachi says that the news of his resignation offer is likely to provide fresh ammunition to anti-India hawks in Pakistan.
Throughout Mr Advani's visit, the hawks had kept asking whether his conciliatory comments were sanctioned by his hardline allies back home.
His resignation offer reinforces their traditional argument that "Hindu organisations" can never shed their reservations regarding Partition.
This is Mr Advani's third term as party president. He already acts as the leader of the opposition in parliament.
If you would like to send a comment about this story you can use the form below this selection of comments.
With all the anti-Jinnah/Pakistan comments and sentiments floating around (expecially after Advani's visit to Pakistan): I wonder whats the point of these confidence building measures and peace initiatives in the face of such intolerance. I don't think this new found love is going to last very long with this attitude.
Mr Advani appears to be a politician who has two faces: one for his hardliners in India and one for the world. Its good he is stepping down.
Mr. Advani has done what no politician in India has the spine to do it. He has proven himself to be a daring Leader who believes in peace.It was his party who Started the Peace process with Pakistan and not Mr. Vajpayee but he deserves the credit.No matter how Indians feel about Jinnah, he was a true Secularist.Muslim League could have never managed to get Pakistan on its own. Pakistanis owes all they have to Mr. Jinnah. Bravo Mr. Advani, India is lucky to have a leader like you.
K.M Sheikh, USA
The hue and cry by various organisations, both the so called "secular" and the "communal", is totally unwarranted and shows a total lack of any sense of history.
It is a well established fact that Jinnah was committed to Hindu-Muslim unity and considered himself the bridge between the communities till the 1937 session of Indian National Congress. He tried hard to drive a compromise between the demands of the hardline Muslim league and what was acceptable to the Congress. But he failed because his own ego and ambition to lead the nation was thrashed in the face of the rise of Mahatma Gandhi as the new popular leader of the freedom struggle.
Shivi Krishna, India
Mr. Advani's remarks could not have come at a better time, when thinking in both India and Pakistan is geared towards bringing peace between the two countries.
A.O. Camara, The Gambia
It's ironic to read that Mr Advani has given such statement about Jinnah. It's no more than an excited mind of an politician, like others who are used to using the immediate environment to develop his future by hiding the truth.
LK Advani has become a wolf in sheep's clothing. He wants to be portrayed as a peaceful politician with no hidden agenda... he can never be trusted.
I strongly believe that the founder of Pakistan was a moderate, secular leader who fought for Pakistan not because the South-Asian Muslims enjoyed their religion, Islam, but because the South-Asian Muslims were not enjoying their social & economical rights under the British subjugation which could later be turned out as Hindu subjugation if partition of India would not have taken place. Mr Advani has been true in expressing RIGHT things about this great Islamic republic's founder.
Asmar Ahmad Atif, Pakistan
It is a shame that Mr Advani enjoyed power for six years riding on the Ram temple issue even though he was "sad". He should have retired from public life on 6 December 1992. I wish to know whether he was happy on 14th August 1947 or the day as home minister of India, he allowed the release of Masood Azhar from jail.
Anshuman Lath, India
While the question of whether Jinnah was a secularist or not is an open question (I personally think he was a political opportunist), I do think that the RSS etc are making much ado about nothing. Pakistan and Bangladesh are separate countries now - if Advani said something to make his hosts feel better about their past, so be it - lets move on !!!
Mr. Advani proved to be very brave for what he said in Pakistan. Before his visit, he was considered to be an extremist by majority of Pakistanis. However, his visit has changed that perception significantly. It looks like Mr Advani is trying his best to further improve the friendship environment between both countries and his statements are linked to his good intentions.
The hardliners should learn the lesson, from the last 58 years of enmity between India and Pakistan, that it is by no means healthy for South East Asia. We must adopt a flexible and friendly attitude towards each other. Mr Advani is trying to do it and the moderates in India must come for his support.
India is considered secular and democratic but I am shocked with the type of democracy it is if a leader of India praises Mohammad Ali Jinnah and becomes the victim of ruthless critism from political parties and press. If Indians cannot tolerate positive comments for the founder of Pakistan from their leader, how can peace be restored or confidence can be established between Pakistan and India.
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