WASHINGTON — The human rights picture in many countries remained deeply troubling last year, the State Department said Friday, with the Middle East facing “the harsh realities of incomplete and contested transitions,” Russia and Iran cracking down on activists, and many governments harshly suppressing both new and traditional media.

For countries undergoing wrenching transitions, in the Middle East or elsewhere, “the way forward is much less clear” than before, said Secretary of State John Kerry, in releasing the department’s annual report on human rights practices at a briefing for reporters.

It was a difficult year for nongovernmental organizations, journalists and bloggers, including ordinary civilians using social media, to vent sometimes daily complaints. The report said that 2012 was the deadliest year for journalists since at least 1997; and that the number of journalists in prison had more than quadrupled since 2011.

But the State Department report also highlighted a few bright spots: Myanmar, formerly Burma, which continued a move away from authoritarian rule; Georgia, which had a rare peaceful transfer of power; and Tunisia, which secured some gains from its 2011 rebellion.