The action came after talks with the radicals broke down.
The BBC reported loud explosions and gunfire were reported as the troops met with stiff resistance. There also were reports of deaths among the radicals, while some children escaped from the complex.
There were concerns about the safety of women inside, who authorities have said were being held hostage.
The New York Times quoted military officials saying the government forces had taken positions on the mosque's roof and also had gained access to the building of a women's religious school attached to the complex.
Negotiations with the radicals were conducted by a group of politicians and clerics through cell phones. Pakistan President Pervez Musharraf had warned those in the mosque would be killed if they didn't surrender.
Abdul Rashid Ghazi, the mosque's cleric who led the standoff, has said about 1,900 people were inside but that number hadn't been confirmed.
The standoff started last Tuesday following gun battles in which several people were killed. About 1,200 students had surrendered.
The militants inside reportedly want Islamic law imposed on Islamabad.