The seizure of the police comes as critics accuse Musharraf of appeasing religious vigilantes, despite concerns that religious figures intent on enforcing a stringent version of Sharia, or Islamic law, have been gaining influence in Pakistan.
Masked students briefly blocked a road near the seminary during a standoff with police.
Religious leaders at Lal Masjid have held an anti-vice campaign since March, bringing them into conflict with the administration of Pervez Musharraf, Pakistan's president.
Monday's abduction followed the seizure of four policemen by students on Friday.
Those officers were abducted as they stood near study centre, according to Abdul Rashid Ghazi, a senior cleric at the Lal Masjid.
One police chief said Ghazi had freed two policemen on Sunday after talks with officials.
He did not say when the two remaining policemen were expected to be freed.
In April, female students at Lal Masjid kidnapped an alleged brothel owner and forced her to make a confession as part of an anti-vice campaign.
The mosque later declared it had set up its own Sharia court, and threatened to close many music and film shops.