Egypt's journey to democracy is proving anything but smooth as clashes between an agitated population and its temporary military rulers continue.

Human rights groups estimate about 40 people were killed last month in clashes with authorities; about 15 were said killed in Cairo just last week.

Egyptian soldiers have raided the offices of more than a dozen pro-democracy, non-governmental organizations -- including three U.S. organizations -- amid accusations of foreign incitement of the protests rocking the capital.

And with Egypt's complicated election process rumbling on for months yet, the situation is unlikely to calm significantly.

"It (the raids on NGO offices) is the clearest indication yet that the Supreme Council of the Armed forces … has no intention of permitting the establishment of genuine democracy and is attempting to scapegoat civil society for its own abysmal failure to manage Egypt's transition effectively," David Kramer, the president of Freedom House, was quoted as saying.

Freedom House is a U.S. international organization promoting human rights and democracy. Its office in Cairo was one of about 17 raided this week by Egyptian authorities.

Egypt's military took control of the country after President Hosni Mubarak, who had ruled the country since 1981, resigned in February amid violent pro-democracy demonstrations and concomitant pressure from the United States -- Mubarak's long-time ally.

Although elections are taking place in Egypt -- for the lower house of Parliament and later a new president -- and the military has pledged to fully relinquish power to civilian authorities by the middle of next year -- it is being suspected of attempting to retain its power in Egyptian society.

The protests taking place in Cairo are against military abuses of civil rights and for immediate handover of power.

Ironically, Islamist organizations which were long opposed to the Mubarak's heavy-handed regime and played a key role in its demise, are apparently not part of the latest ground-swell of demonstrations. If the military, in reaction to civil disorder, were to cancel the balloting taking place around the country they would lose out on dominating any new, permanent civilian government.

In the first round of voting recently, Islamists won the largest vote. The Freedom and Justice Party of the Muslim Brotherhood garnered 36 percent of ballots cast in the party-list vote and about 32 of the 56 individual parliamentary seats up for grabs. The more fundamentalist Salafist party Al-Nour won 24 percent of the ballots cast and five individual seats.

Secular parties and candidates trailed.

The second round of voting is taking place in mainly rural sectors, where the Islamists are again expected to do well.

Protests in one form or another have become common in post-Mubarak Egypt. The latest explosion in Cairo was sparked by military authorities breaking up a sit-in outside Cabinet offices. Severe beatings of protesters took place.

The public outrage when photographs and videos of the beatings appeared on social networking sites, then spiraled.

Military authorities apologized for the mistreatment but followed with the raid on NGO offices. The military had earlier accused foreign elements of stirring up dissent, even through the illegal funding of Egyptian political organizations.

The beating of demonstrators, particularly female demonstrators, resulted in a stern rebuke from Washington, which provides the Egyptian military with more than $1 billion in aid annually.

Meanwhile, Mubarak this week again was hauled into court in Cairo, where he faces a multitude of charges, including graft and corruption. The appearance could likely stoke further protests against the military -- Mubarak's ally and tool during his reign -- as it brings more focus on the military's past, present and future in a new Egyptian political landscape.