According to Dawn Online, the two also discussed matters of internal security and the war against terrorism.
The cleric vowed to seek justice for 14 of his supporters killed in a police raid last year.
Pakistan Prime Minister Nawaz Sharif on Tuesday said that India and Pakistan must put aside differences and work for peace.
The Interior Ministry issued an order on Saturday asking all provincial governments not to carry out any executions in the Muslim month of fasting.
Pakistan has been sharply critical of India with its leaders slamming Modi's recent remarks in Bangladesh that Pakistan was creating disturbance and instigating terrorism in India.
He said his country will take all steps to 'expose' India's role in the break up of East Pakistan in 1971 and to 'destabilise' it through terrorism.
Pakistan Prime Minister Nawaz Sharif's ruling Pakistan Muslim League-Nawaz has emerged as the single largest party in the legislative assembly elections in the strategically-located Gilgit-Baltistan region.
The "characterisation of bilateral relations by the Indian PM as 'nuisance' is unfortunate," Pakistan Foreign Office spokesperson Qazi Khalillulah said.
The spy agency had tapped 6,523 phone numbers in February, 6,819 in March, 6,742 in April
Pakistan is expected to discuss with the US, the alleged role of India's external spy agency RAW in abetting violence in the country.
A suicide bomber got within striking distance of Gaddafi stadium where over 20,000 people were watching a Pakistan-Zimbabwe ODI but was foiled by a policeman, who along with a civilian, was killed when the militant blew himself up.
A Pakistani military helicopter carrying 11 foreigners crashed in the Pakistan occupied Kashmir on Friday, killing ambassadors of the Philippines and Norway and at least five others as the Taliban claimed responsibility for the downing of the chopper and said Prime Minister Nawaz Sharif was the target.
The court has fixed May 8 for hearing of the case.
Can Islamic Republic of Pakistan be a secular state?
The court found 4 of the accused guilty and handed down the 25 year sentence.
Our desire for good neighbourly relations with India has not been reciprocated, said Pakistan PM Nawaz Sharif.
Nawaz Sharif will lead a high-level delegation to Saudi Arabia in a bid to cool tempers in the kingdom over Islamabad's refusal to provide troops for the war in Yemen.
Pakistan on Tuesday hanged 17 prisoners, the highest number of executions on a single day
Chinese President Xi Jinping on Tuesday described Pakistan as China's "dependable" friend and firmly backed its territorial integrity
Chinese President Xi Jinping arrived in Islamabad on Monday on his first visit to Pakistan where he is expected to sign a deal for an economic corridor worth $46 billion and other agreement.
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