Addressing the one-day Interior/Home Ministers Conference of SAARC countries here, Khan equated the use of force by Indian security forces with "terrorism".
There is a difference between fighting for freedom and terrorism, he was quoted as saying by local media.
"The violence being committed against the innocent people" of Kashmir is "open terrorism", he said, speaking extempore.
Local media reports said that it seemed Khan decided to ignore the written notes in order to respond to the speech of Home Minister Rajnath Singh, who without naming Pakistan lambasted it for supporting terrorism.
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Khan said Pakistan suffered heavy losses in the fight against terrorism and the country condemned every single incident of terror which claimed innocent lives.
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Later, while addressing a media briefing, Khan said he responded to Singh's speech at the SAARC conference to "put the record straight" on the issue of terrorism.
"When someone tries to cast aspersions on Pakistan, then it becomes necessary to clarify our stance and position," he said.
Khan said Rajnath had not named Pakistan but his intentions and target was clear.
"I said that not only terrorist attacks in Dhaka, Mumbai and Pathankot should be condemned but also those committed in Peshawar, Karachi and Lahore," he said.
"I also said that there is blatant foreign intervention in Pakistan across from the borders but we do not raise a storm," he said.
He also said that the meeting of SAARC ministers was successful and all agenda items were discussed. Khan said the next meeting would be held in Sri Lanka in 2017.
A statement issued by Pakistan's Interior Ministry said, "Khan called on regional countries to differentiate between terrorism and freedom movements sanctified by the UN Security Council."
"The Interior Minister highlighted that Pakistan itself has been the biggest victim of terrorism and instead of engaging in a blame game and taking swipes at each other we should take time out to reflect and sit down together and try to work out the problems and reservations which we might have towards each other," the statement said.