The bonds are an alternative approach to mass arrests, which Pakistan used last year in an unsuccessful crackdown on armed groups.
"They are being asked to give surety bonds of good behaviour. If they violate them we will arrest them and their surety will be forfeited," a senior police intelligence official said on condition of anonymity.
Nearly 600 activists of armed groups outlawed on Saturday have been ordered to pay security bonds of up to 100,000 rupees ($1,725), he said.
"This strategy is different to previous attempts when large-scale arrests were made because most of those people were subsequently released by courts," he added.
Four of the five groups outlawed by President Pervez Musharraf in January 2002 under his high-profile anti-Islamist crackdown re-emerged under new names. Most of their 2000 followers and leaders were released after several months in jail.
"If they disobey the government ban again they will be punished"
Faisal Salih Hayat,
Interior Minister, Pakistan
Three of the groups were banned again on Saturday and a fourth was placed under surveillance under a new anti-Islamist drive.
Authorities have since shut down 137 offices of the banned groups and arrested one of their leaders, although his arrest was related to the murder of a hardline Sunni leader in early October.
Interior Minister Faisal Salih Hayat said the government had chosen to seek "guarantees" from the Islamists instead of arresting them as "a new strategy".
"We are not going for the arrest of members of these banned groups," he said.
"We are closing down their offices to deny them a forum. We are seeking guarantees from them that they do not indulge in such activities in the future,” Hayat said.
"This is providing them an avenue to correct their behaviour. If they disobey the government ban again they will be punished," he added.
The groups outlawed on Saturday were Islami Tehreek, the Shia armed group formerly named Tehreek-i-Jafria; Khudamul Islam, the new name for the Jaish-e-Muhammad fighting Indian rule in disputed Kashmir; and Millat-e-Islami, which was earlier the armed group Sipah-e-Sahaba.