Pakistan Foreign Minister Khurshid Mamhud Kasuri and his Indian counterpart Natwar Singh shook hands before sitting down for the talks at a national guest house in the Indian capital.
The meeting was preceded by sharp exchanges between the two sides, with New Delhi accusing Islamabad of being "unifocal" in its approach to Kashmir and saying cross-border insurgency had to end before real progress could be made.
At issue was a statement issued by Kasuri Saturday before flying to New Delhi in which he restated Pakistan's long-held positions on Kashmir and called for "courage and boldness" to resolve the row.
He also all but accused India of merely going "through motions" and of not being serious in trying to find a solution to the dispute over Kashmir, which is divided between India and Pakistan but claimed in full by both.
Indian foreign ministry spokesman Indian Navtej Sarna hit back late Saturday.
"There is considerable disappointment here at the unifocal statement by the Pakistan foreign minister earlier today (Saturday) about relations with India prior to his departure from Islamabad," Sarna said in a statement.
Going into the talks Sunday, Kasuri attempted to play down the spat.
"We have come here with a positive frame of mind to review the progress on the Composite Dialogue," he told reporters.
The Composite Dialogue is the label given to talks between officials of the two sides since March aimed at building consensus on eight major issues which have been points of discord between the rival neighbours since independence from Britain in 1947.
"I read some of the comments of the newspapers here and let me tell you we are not unifocal because if we want peace in South Asia both countries have to make up their minds," Kasuri said.
India's Natwar Singh also tried to play down the row.
"I share his sentiments as we are committed to have cordial and friendly relations with Pakistan. It is in our interest to have peace and amity," Singh said after shaking hands with his counterpart from across the border.
India accuses Pakistan of arming and training Islamic guerrillas in Kashmir, an allegation Islamabad denies although it openly offers diplomatic support to what it calls the Kashmiris' rightful struggle for self-expression.
More than 40,000 people have died in Indian Kashmir since the launch of the rebellion there in 1989.
On Saturday, Prime Minister Manmohan Singh said ties can improve if Pakistan discusses issues besides Kashmir and halts the flow of rebels into Indian Kashmir.
"We are not afraid of discussing Jammu and Kashmir but we do not buy the argument that it is the only issue affecting relations between our two countries," Singh told a press conference.
"The dialogue can only move forward only if terrorism is under control," he added.
Foreign secretaries from both countries on Saturday said they had agreed to broaden the peace process after approving a slew of proposals to be presented to the ministers on Kashmir and strengthening ties.
New Delhi, however, has cautioned against expecting too much to come out of the ministerial talks.
A summit between Pakistan President Pervez Musharraf and then Indian premier Atal Behari Vajpayee collapsed over Kashmir in 1999 but ties warmed in April last year after the Indian leader extended a "hand of friendship" to Islamabad.
The two South Asian rivals who armed themselves with nuclear weapons in 1998 have fought two of their three wars since independence in 1947 over Kashmir and came close to a fourth full-scale conflict two years ago.