The deadline is for the "mosque administration to surrender [and] hand over their weapons" Anwar Mehmood, Pakistan’s information secretary, said.
"At the moment law enforcement agencies are exercising restraint... they are not going to fire until they are fired at… The men who surrender will be ensured safety."
Negotiations to end the siege of the mosque, brokered by independent clerics, "appear to heading nowhere", Abdul Rashid Ghazi, deputy leader of the students, said.
"First they should stop this action and only then there could be any negotiations," he said.
Deaths in hospital
Three other wounded students were treated at the state-run Pakistan Institute of Medical Sciences early on Wednesday, a doctor at the hospital's emergency ward said.
Three people, critically wounded in the previous day's fighting, died overnight, the doctor said.
Three others with serious bullet injuries were brought to another state-run hospital, the Polyclinic, a doctor there said.
"One of them is undergoing surgery at the operation theatre," he said.
As well as the deaths, more than 120 were wounded in the fighting on Tuesday, officials and hospitals said.
Violence began at the mosque when around 10 students, armed with staves, attacked a police party which was taking up positions around the mosque.
Police then fired teargas at the students, prompting an exchange of gunfire lasting around 15 minutes, witnesses said.
Appeals were made on the mosque's loudspeakers for residents of Islamabad to come to the mosque and help the students and 'mujahideen'.