NSA Ajit Doval, Foreign Secretary S Jaishankar and some other officials were present in the meeting that took place at the Prime Minister's residence.
The arrests come soon after U.S. President Donald Trump's administration cited Pakistan's strict blasphemy laws in a message warning American citizens against traveling to the Muslim-majority nation.
"The two sides discussed a range of bilateral and regional issues".
Mr McMaster and Mr Doval have held detailed discussions on Indo-US relations especially the security aspect of the ties.
President Trump had seemed inclined to act tough on terrorism in the early days of his inauguration-with the White House readout of a conversation Trump had with Indian Prime Minister Narendra Modi in January stating that "Trump and Prime Minister Modi resolved that the USA and India stand shoulder to shoulder in the global fight against terrorism".
During his meeting with Prime Minister Nawaz Sharif in Islamabad, the US NSA had hinted that Washington could take a tougher stance on Pakistan, said sources.
Incidentally, McMaster's visit to Afghanistan came just a day after the USA dropped its biggest non-nuclear bomb on Nangarhar province of that country, killing some 100 IS militants.
Sharif said as a longstanding friend and a partner, Pakistan was looking forward to forging a strong and mutually beneficial partnership with the U.S. and to working with the new Trump administration, to promote peace and security in the region and beyond.
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McMaster - a U.S. Army general who served in the American-led worldwide force in Afghanistan - indicated frustration with Pakistan in an interview with an Afghan news channel on Sunday.
Sharing his concerns over the deteriorating security in Afghanistan and the continuing impasse, Sharif conveyed Pakistan's readiness to work with the global community to explore ways to solve the Afghan crisis, it said.
During his meeting with McMaster, Sharif stated that across-the-board consensus was achieved by his government to combat extremism and terrorism, the PMO statement said.
Earlier, McMaster-led United States delegation approached Adviser on Foreign Affairs Sartaj Aziz at the Ministry of Foreign Affairs here.
"As all of us have hoped for many many years, we have hoped that Pakistani leaders will understand that it is in their interest to go after these groups less selectively than they have in the past and the best way to pursue their interest in Afghanistan and elsewhere is through diplomacy not through the use of proxies that engage in violence", McMaster said in an interview with Afghanistan's Tolo News Sunday.
A statement from Sharif's office quoted the prime minister as saying that Pakistan is looking forward to "forging a strong and mutually beneficial partnership with the US" and working with the new United States administration to "promote peace and security in the region and beyond".
As part of the South Asia trip, he also visited Afghanistan before travelling to Pakistan. For India, there are concerns about the peace process in Afghanistan being hijacked by Pakistan or being influenced by what New Delhi sees as a closer cooperation between Pakistan and China.
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