Musharraf said: "The government has enough power and no-one can stand before its might. Our concern is for children and women and we are showing a lot of patience and restraint.
"They have defamed Islam, they have defamed Pakistan, they have embarrassed Pakistan internationally."
Al Jazeera's Rageh Omaar, who is outside the mosque, said many woman and children were believed to still be inside.
"Up until now the government's position had been that it was very reluctant to storm the mosque or take any military action until all women and children were out," he said.
"That was a position repeated at a cabinet meeting ... but it is of course president Musharraf's words that hold ultimate sway."
Ghazi has rejected government accusations that the women and children inside are being held as human shields.Fresh clashes
Fresh clashes earlier on Saturday prevented a group of Muslim leaders reaching the compound and attempting to negotiate an end to the standoff.
The five-member delegation from religious parties blamed the security forces for starting the shooting to stop them from getting in.
|Workers have cut off electricity, gas |
and water to the Red Mosque [AFP]
"Security forces are not allowing us to go in and they have opened fire," Samia Raheel Qazi, a member of parliament, said.
"Whatever happens now, the government will be responsible."
The delegation had received permission from Abdul Rashid Ghazi, the senior cleric at the mosque, to enter the compound and was hoping to persuade him to send out children.
Officials say they do not know how many students are left inside but they estimate that there are up to 60 "hardcore" armed men.
Ghazi has said 1,900 people remain in the compound.
Water, gas and power to the mosque have been cut in an attempt to force more students out. Food was said to be getting scarce.
The goverment has that 19 people have died during clashes around the mosque, but Ghazi claims that Pakistani forces have killed up to 30 female and 40 male students during the siege.
Police also seized control of the nearby Jamia Faridia, an Islamic seminary affiliated with the Red Mosque, on Saturday.
Authorities said they feared that students from the seminary, three kilometres from the mosque, would open another front as the confrontation entered its fifth day.