Scaf generals say they will have final approval over new political system, whatever the outcome of the election

Egypt's ruling generals have put themselves on a collision course with the country's new parliament after declaring that MPs will not have the final say over the drafting of a fresh constitution.

The revelation is likely to escalate tensions once again between the Supreme Council of the Armed Forces (Scaf) and an increasingly confident Muslim Brotherhood, which looks set to dominate the new assembly once voting is completed and parliament opens for business, in March.

Millions of Egyptians have flocked to the polls in recent days to elect parliamentary representatives, whose primary role is to appoint a special body tasked with drawing up Egypt's first post-Mubarak constitution. But after initial results indicated that political Islamists will form a majority in the new chamber, the military has moved swiftly to rein in their powers and ensure its own well entrenched political and economic privileges remain intact under any future civilian government.

In a rare interview with foreign media, Major General Mokhtar el-Mulla – a leading member of Scaf – said the upcoming parliament would not be representative of all Egyptian people, and that those appointed to write a fresh constitution must also be approved by the interim cabinet and a newly-created "advisory council" of intellectuals, civilian politicians and media personalities, both of which fall under the control of Scaf.

"This is the first stage in our democracy," said Mulla, who also insisted that details of the army budget must remain shielded from democratic oversight, even after the generals return to their barracks. "In the future, parliament may have the ability to do whatever it likes. However at the moment, given the unstable situation, parliament is not representing all the Egyptian people."

"This is not out of mistrust of the parliament," he continued. "What we are seeing is free and fair elections ... but they certainly don't represent all sectors of society."

His comments came as Kamal el-Ganzouri, Egypt's military-appointed transitional prime minister, unveiled a new cabinet and claimed he had been granted 'presidential powers' by Scaf, which assumed power following the toppling of Hosni Mubarak in February. But el-Ganzouri admitted that oversight of the judiciary and the army remained off-limits to the government, and his new ministers were instantly rejected by anti-junta protesters who continue to occupy parts of central Cairo in an effort to force an end to military rule.

After weeks of deadly violence between security forces and revolutionaries, who accuse Scaf of being little more than an extension of the old Mubarak regime, Mulla used a long and often heated meeting with the international press to deny claims that Egypt's so-called "democratic transition" was under threat. He said that the process of writing a new constitution would begin in April next year, and that the document would then be put to a public referendum in June ahead of presidential elections later that month.

"By 30 June we will have an elected president and the army will have only one role to perform, which is to protect the country," said Mulla. "[Beyond this] Scaf does not seek continued authority, and we will not interfere in political life."

He acknowledged that the timetable had been designed to prevent any "specific groups" – a thinly-disguised reference to Islamists – dictating the country's political future for decades to come, but dismissed suggestions that the army's stance could provoke a backlash from the Brotherhood and other democratically elected civilian political groups which had been expecting to control the constitution-writing process themselves.

"If you look back at the history of Egypt, you can see we have been occupied by the British, the French, and the Ottomans," said Mulla. "None of them were able to alter the basic features of the Egyptian people, and whoever forms a majority in parliament also won't be able to alter those basic features … the Egyptian people won't allow this to happen."

Despite promising a "completely free" discussion with journalists – who are rarely offered access to Scaf, an institution often shrouded in secrecy – Mulla clashed several times with reporters over questions regarding the army's role in recent assaults on demonstrations, which have left more than 40 dead and thousands injured.

He acknowledged that the military had ultimate control over security affairs in Egypt at the moment, but said that the armed forces would never commit violence against the Egyptian people and rubbished evidence provided by doctors and human rights groups suggesting that live bullets had been used against protesters. "What was mentioned and said in the media concerning the recent incidents in Tahrir [Square] was totally wrong," claimed Mulla. "What should the ministry of interior do when attacked with molotov cocktails and stones? Of course the responsibility of the ministry is to defend itself according to the law. Their troops have the right to use live ammunition … but honestly they didn't resort to this."

The Major General refused to discuss the case of imprisoned blogger Maikel Nabil, who was found guilty by a military tribunal of insulting the army earlier this year and has remained behind bars and on hunger strike ever since. On Wednesday, Nabil's trial was delayed for the fifth time, and is now due to commence on 14 December.

"No one has been brought in front of court based on their opinion or activity on Facebook, Twitter or any other media," said Mulla, ignoring Nabil's case. When challenged on this he refused to comment further, and accused the media of "fixating" on detained bloggers including revolutionary figurehead Alaa Abd el-Fattah, who is behind bars for alleged crimes committed during the protests outside the state television headquarters in October.

"The media has ignored the [charges of] crimes against [Abd El Fattah] and concentrated instead on him being a blogger and activist," concluded Mulla. "Maikel Nabil and Abd el-Fattah are Egyptians and we are very keen to protect all Egyptians. But we are talking about one citizen out of 85 million Egyptians."