The separatists crossed over into Pakistan by foot
Indian Prime Minister Manmohan Singh has accused Pakistan of violating travel agreements during a recent visit to Pakistan by Kashmiri separatists.
Moderates from the disputed territory made the landmark trip earlier this month in a visit opposed by hardliners.
They crossed the Line of Control into Pakistani-administered Kashmir from the Indian-controlled side.
But India has criticised Pakistan for allowing them to move beyond Pakistani-administered Kashmir.
"That Pakistan decided to invite them to visit Islamabad and other cities in Pakistan violated an understanding on these procedures that had been reached between India and Pakistan," Mr Singh said.
But Pakistan's Information Minister, Sheikh Rashid, says he was not aware of any agreement that prevented the separatists from visiting Pakistan.
"The idea was to create an opportunity for them to speak to the Pakistani leadership," he told the BBC News website.
"It was a way of bringing the party that is most affected by this conflict - i.e. the Kashmiris - into the ambit of what is being discussed between Pakistan and India."
The Indian prime minister was replying to criticism by former prime minister Atal Behari Vajpayee that the visit had been mishandled by the Indian government.
India had issued passports to the separatist leaders but reports say they were permitted by Pakistan to travel across the country without visas or the use of their Indian passports.
In a letter to the Indian prime minister last week, Mr Vajpayee said the separatists' visit to Pakistan was "against the established norms of international travel".
He also criticised the prominence given to the separatists despite there being an elected government in Indian-administered Kashmir.
But Mr Singh has defended his actions saying that his government recognises that there are some groups in Kashmir which are outside the electoral process.
"We are nevertheless willing to enter into a dialogue with such groups, provided they agree to abjure the path of violence," he said.
The separatists' visit came 18 months after India and Pakistan launched a peace process.
The separatists described the visit as a major success and the first step in involving Kashmiris in the peace process.
But on Monday, an Indian minister said the separatists would not be allowed to join the peace talks.
Junior home minister Sri Prakash Jaiswal said the separatists could hold separate talks with the government but would not be given third party status.
The comments have been criticised by Kashmiri separatists.