Egyptian civil society groups unregistered under any law will be facing a "worrying condition” according to words from the ministry of social solidarity, hours after an ultimatum was given to these groups to register under a controversial NGO law expired on Tuesday.

The civil groups have been facing uncertainty since the government announced an ultimatum to register under the 2002 NGO law, deemed restrictive by critics and observers.

The ultimatum ended on Monday, prompting some groups to close their offices or halt their activities. NGOs that did not register were expected to face harsh criminal charges.

For decades, many entities were registered as civil companies or legal firms to escape the provisions of the 2002 law, which they say gives the government a wide range of authority over the activities and the funding of rights and civil groups.

Other groups had no authorisations under any law whatsoever.

"The ministry will not… go after the entities that practice civil work under any Egyptian law, either that of the NGOs of 2002 or any other law," social solidarity minister Ghada Wali was quoted as saying to state-news agency MENA.

Wali said the ministry will, however, address the unauthorised groups to inquire about their operations and funding.

"Legal action against these groups is still being studied," Wali said.

Egypt faced wide criticism from several countries in its human rights review in front of the United Nations in Geneva last week over the status of NGOs, while seven groups cancelled their meetings planned on the sidelines of the event citing a "hostile environment to the work of NGOs."

The ultimatum given to register under the old law comes at the same time a new law is being drafted. 

The government says the registration, as per a Hosni Mubarak-era law, is meant to ensure transparency in NGO funding and activities so they are not used as a front for illegal conduct.

During the Geneva conference, officials said there will be no final draft for the new NGO law until a new parliament is elected, expectedly by the first half of 2015.

Wali's comments on Tuesday were seen, however, as a positive step by many.

A mediator in the NGO-government talks, Hafez Abou Saeda said the allowance of being registered under a different law opened up an "opportunity for negotiations."

He said the latest round of NGO-governmental talks has been fruitful, producing a near consensual draft with the social solidarity ministry. It is up to the ministry when to make it public, he EXPLAINED.

The latest version of the draft, made public in July, was disappointing to NGOS and caused an uproar.

"I understand the fears of the groups…but I think a common ground could be reached until the new law is passed," Abou Saeda told Ahram Online.

 "All the parties agree that a new form for the NGOs law has to be out,” Saeda added.

Abou Saeda's group, the Egyptian Organisation for Human Rights (EOHR), which has been registered as a NGO since 2002, has called on the ministry to extend the ultimatum until the new law is issued.

"Enacting the decision of social solidarity ministry is ravaging the right to assembly and association and is inconsistent with international conventions and the Egyptian Constitution," EOHR said on Monday.

Local and international human rights organisations have been the subject of constant intimidation and security surveillance for decades under the rule of Mubarak.

They have been regularly harassed, contested and accused of spying in the three years following the 2011 popular revolt which toppled Mubarak.

In December 2011, at least 17 Egyptian and US groups’ offices were raided on accusations of "conspiring against the state" and later 43 of the NGOs' employees were tried and given prison sentences for running unlicensed organisations, receiving foreign money and conducting political training without permits.

Fears were renewed after an amendment to article 78 of the penal code, stiffened regulations over foreign funding, on which many of these groups depend.

The article amended in September by a presidential decree states that offenders who receive foreign or local funding or items to commit acts against the state's interests, "shall be punished by life imprisonment and a fine no less than 500 thousand Egyptian pounds and no more than what he has been given or promised."

This punishment could be raised to execution if the perpetrator is a public servant or holds a public representative status, or "if he committed the crime at wartime or for the purpose of terrorism."