The warnings came after Hamid Karzai, the president of Afghanistan, threatened on Sunday to attack pro-Taliban fighters on Pakistani soil, saying his country had a right to do so in self-defence.
His statement came after an air raid launched by US-led forces based in Afghanistan killed 11 Pakistani soldiers in the Mohmand tribal region last week, according to Islamabad.
"When they cross the border from Pakistan to come and kill Afghans and coalition troops, it gives us exactly the right to go back and do the same," Karzai said.
"It's very easy for him [Karzai] to place blame and not take any serious responsibility of his own," General Talat Masood, a retired Pakitsni general and former secretary of defence, told Al Jazeera.
"There is, of course, also certain cross-border movement from Pakistan," he said, but suggested there were more pressing issues that were preventing peace in Afghanistan.
"There is [also] a lack of co-operation between the United States and Pakistan at the moment they see things very differently. They [the US] are opposed to Pakistan trying to have negotiations with tribal leaders - they don't like that, they would like the military pressure to be continued."
Pakistan's Prime Minister, responding to Karzai's speech, said: "Such statements will not help in the normalisation of friendly relations between the two countries and will hurt the sentiments of people on both sides of the border.
"We will neither interfere in the internal affairs of any country, nor will we allow anyone to interfere in our affairs."
'Violation of sovereignty'
Gilani said that Pakistan was taking all possible measures to stop fighter activity across the long, rugged frontier between the two countries.
He also said he wanted "friendly" ties with Kabul.
Islamabad says it has more than 90,000 troops in its tribal regions along the border with Afghanistan and that 1,000 soldiers have died fighting there since 2001.
Pakistan has strongly opposed any foreign military action on its soil, saying it would amount to a violation of its sovereignty.
"We are not fighting this war for America but it is our own war and we want to eliminate extremism and terrorism which is the root cause of all evils," Gilani said, in his comments carried on the privately-owned ARY-OneWorld television.
Afghan and Western officials have repeatedly accused Pakistan of failing to do enough to stop pro-Taliban and al-Qaeda-backed fighters operating on its territory.
They have also expressed concerns over the government's recent negotiations with Taliban fighters.