Members of Pakistan's six-party Islamic alliance (MMA) walked out of parliament on Friday in protest at breakthrough talks between Pakistan and Israel.
There was a low turnout at protest rallies in most of the country
However there was a muted response to MMA calls for widespread protests in cities across the country.
Pakistan says Thursday's meeting, held in Turkey, does not mean it recognises the state of Israel.
It says that the talks were initiated at the request of the head of the Palestinian Authority Mahmoud Abbas.
MMA supporters held protests at the talks outside several mosques across the country but they failed to attract many people, according to the BBC's Zaffar Abbas in Islamabad.
The biggest protest was held in Peshawar, provincial capital of North West Frontier Province led by MMA President Qazi Hussain Ahmed.
Around 200 protestors carrying placards and banners chanted slogans against the US and against the government of President Musharraf, the BBC's Haroon Rashid in Peshawar says.
In Karachi, Pakistan's largest city, there was barely any protest.
Correspondents say that the low response may indicate a larger preoccupation with domestic issues.
Qazi Hussain Ahmed told the BBC News website on Thursday that the move to hold discussions with Israel went "against Pakistan's national interest as well as state policy."
The West Bank leader of the Palestinian militant group, Hamas, has also condemned the meeting.
"We condemn any relationship between an Islamic state and the Israelis and we ask Pakistan to go back on this agreement, especially as the Palestinian people have not yet been given their rights," said Hassan Yussef.
In Gaza, hundreds of supporters of Islamic Jihad, a Palestinian militant group protested against the Israeli-Pakistani talks.
'No fundamental change'
But the president of Pakistan's ruling party, the Pakistan Muslim League, said that Pakistan was seeking to help the Palestinians.
"It's very strange that marriage with Jews is a right but talking to them is wrong," Chaudhry Shujaat Hussain said.
About 200 people took part in the protest in Peshawar
Prime Minister Shaukat Aziz told parliament that Palestinian leader Mahmoud Abbas had called on Pakistan to take a more active role in the resolution of the Israel-Palestinian conflict during a trip to Islamabad two months ago.
Soon after, the Turkish prime minister offered to arrange a meeting between the foreign ministers of Israel and Palestine.
After the talks, Pakistan's Foreign Minister Khurshid Kasuri said that his country had decided to "engage" with Israel after Israel's withdrawal from Gaza.
Muslim states that have relations with Israel
Israel's foreign minister described the talks as a "historic meeting".
Silvan Shalom told Israel Radio: "We are talking about a tremendous significance, not just in regards to our relations with Pakistan, but the entire Muslim world."
He said that he hoped the talks would lead to "a full diplomatic relationship with Pakistan, as we would like it with all Muslim and Arab countries".
Before the meeting, Pakistan's President Musharraf spoke to Palestinian President Mahmoud Abbas and to Saudi Arabia's King Abdullah. Both supported the move to hold talks, Pakistan says.
Pakistan has previously linked the question of its recognition of Israel to the establishment of a Palestinian state.
But in July 2003, President Pervez Musharraf called for a national debate on the possibility of opening diplomatic ties with Israel.
The BBC's Aamer Ahmed Khan in Karachi says the sensitivity that surrounds any move towards establishing diplomatic ties with Israel is evident from the choice of the word "engagement" rather than "relations".