The Brotherhood’s Freedom and Justice Party (FJP), which has promised to work with a broad coalition in the new assembly, secured 34 individual seats out of the 45 it contested in the run-offs on Monday and Tuesday, a party source told Reuters.

Official results are not expected until Thursday.

A total 56 individual seats were up for grabs in the first round of the election, with others assigned to party lists. Two more rounds follow, with the last run-off set for mid-January.

Salafis were the surprise runners-up in the opening stage of the ballot but the Islamist rivals are playing up their differences, giving liberals scope to take part in a post-election government and shape the future constitution.

The conservative Brotherhood’s early lead will disappoint many of the democracy activists who led protests that toppled President Hosni Mubarak in February, but it confirms a trend set by Islamist election wins in post-uprising Tunisia and in Morocco.

It has also unnerved Israel, which called on Egypt this week to preserve their 1979 peace treaty, and the United States which has backed the peace deal with billions of dollars in military aid for both countries over the past three decades.

The Brotherhood has emphasized the political reform agenda it shares with a broad range of groups that took part in the uprising, playing down the socially conservative agenda usually associated with Islamist movements.

The FJP already secured two clear-cut wins for its individual candidates last week and its party list won 36.6 percent of valid votes, with the Salafi party al-Nour’s list second at 24.4 percent. Two thirds of parliament seats will be assigned proportionally to party lists.

Brotherhood leader Mohammed Badie has also denied suggestions that Islamists would tussle with the army generals who took control when Mubarak was overthrown.

Parliament’s popular mandate will make it difficult for the military council to ignore, but the army will keep hold of the levers of power until a presidential election in June, after which it has said it would hand over power to civilians.

The army announced on Tuesday it would give more decision-making powers to its newly-picked prime minister, Kamal al-Ganzouri, in an apparent attempt to deflate criticism that it is seeking to retain its authority over the political transition.

Ganzouri, tasked with forming a “government of national salvation” after violent street protests last month, announced a new cabinet with many incumbents keeping their portfolios.

But he picked a new finance minister with the tricky job of stabilizing an economy battered by months of unrest and has yet to declare his new interior minister, who will replace a predecessor criticized for failing to reform the police force.