(Reuters) – An attack on the Israeli embassy in Cairo last week could set back political gains since Hosni Mubarak was toppled in a popular uprising this year, as the ruling army council takes measures to tighten security around the country.

Protesters scaled the building where Israel occupies the top two floors, replacing the Israeli flag with Egypt’s and seizing embassy documents from a storeroom on a lower floor before tossing them from a window to cheering crowds below.

The Israeli ambassador and his family fled Cairo that night in an Israeli military helicopter. Israel and the United States issued anxious calls for Egypt to respect its controversial 1979 treaty with Israel and protect the embassy.

Egypt’s government swiftly offered reassurances it would boost security at the embassy and chase down those behind the attack, indicating the treaty was still safe.

But many Egyptians worry the security crackdown that follows will undermine political freedoms gained since the uprising.

Officials have said emergency law, a key plank of Mubarak’s social control mechanisms in place since he took power in 1981, will be reactivated to try those involved in the embassy attack.

“This is the first time since the revolution that they transferred anyone to a state security court,” said Emad Gad of the Al-Ahram Centre for Political and Strategic Studies.

“There is already a bad security situation in the country with crime rising. They (the ruling generals) are taking advantage of this,” he added.

Activists and opposition parties have disowned the violence around the embassy which they say sullies the uprising’s goals.

But the revival of courts under emergency law will be just as worrying. Some of the demonstrators who moved on the embassy had come from a protest on Friday in Tahrir Square where one of the demands was scrapping the hated emergency laws immediately.

Analysts say Egypt’s democratic transition could suffer and some already see worrying signs of a slow return to the kind of tactics used by Mubarak’s security forces to stifle opponents.

Security officers raided offices of the Al Jazeera television channel on Sunday and detained staff in what the Qatar-based broadcaster said was an attempt to drive the channel, which had live coverage of the embassy incident, off air.

Al Jazeera was a target in the last days of Mubarak’s rule.

A security source said several other channels were shut down over licencing or other breaches of professional codes.

FEAR FOR DEMOCRACY TRANSITION

Changes in Egypt have been sweeping since Mubarak was ousted on Feb. 11. His party was dissolved, his hated state security service was revamped and he and many familiar faces from his three decades of rule were sent to trial on charges ranging from corruption to conspiring to kill hundreds of protesters.

But there is a deep sense among many of those who protested against Mubarak that his system remains in place although he has gone. An interim cabinet now answers to a military council headed by Mubarak’s defence minister Mohamed Hussein Tantawi.

Tantawi did not turn up to give testimony behind closed doors at Mubarak’s trial on Sunday, saying he was busy handling the security crisis, state media said. The hearing has been delayed till later this month, fuelling more suspicions.

“This is a sign and it’s possible there could be repercussions for the elections,” said Gad. “They have an interest in delaying — to let figures from the old NDP form new political parties.”

Candidate registration for a parliamentary election is due to open sometime this month ahead of polls expected in November, although no date has been set.

Mubarak’s National Democratic Party (NDP) was a vehicle for the state under Mubarak, whose government viewed most of the Islamist, leftist and Arab nationalist forces that dominate the political scene now as irresponsible opposition who would harm Egypt’s position with the West through populist policies based on enmity to Israel.

Hossam Tamam, a researcher on Islamist groups, said many people feared the ruling military council was looking for reasons to slow the shift to a new system and a security vacuum in the country was serving that purpose.

“The official rhetoric says they want a complete transfer to civilians but, deliberately or otherwise, their policies have led to a vacuum, confusions and no faith in the process. No one knows when or if the transfer will happen,” he said.

AGENTS PROVOCATEURS?

Conspiracy theories have mushroomed since Friday, with many activists, columnists and politicians suggesting Mubarak allies placed agents provocateurs among the protesters to provoke violence that would place the protest movement in a bad light.

They note that a nearby police building was ransacked. Three people were killed and more than 1,000 injured in clashes with riot police that resembled the pitched battles of the uprising.

Nervous looking soldiers stood in the doorway of the embassy building on Monday, as curious Egyptians pored over the rubble of a wall protecting the building that protesters destroyed.

The government erected the concrete barrier after the Israeli flag was removed in a similar protest last month.

“It was here, but it’s gone now,” a teenager said, laughing.

The wall provoked popular anger because it went up after Israel shot several Egyptian soldiers in border operations against Palestinians in Gaza last month.

The government appeared to fumble in its response to that incident, at first saying it had recalled Egypt’s ambassador to Tel Aviv then recanting the claim.

Turkey’s diplomatic jousting with Israel in recent years is making it difficult for Egypt’s generals to follow the same policies of Mubarak, who is widely perceived to have been soft on Israel in tune with his predecessor Anwar Sadat’s shift of Egypt’s political orientation in return for U.S. aid money.

Anti-Israeli graffiti can still be seen daubed on slabs of the concrete walls and other buildings all around the tower housing the embassy: “I want to go to Jerusalem”, “Islam is coming, despite America and Israel” and “Crush the Zionists”.