The city is home to a revered Shiite shrine that was bombed in 2006, sparking a sectarian conflict between Iraq's Shiite majority and Sunni Arab minority that left tens of thousands dead.
The city lies just 110 kilometres (70 miles) north of the Iraqi capital on the main highway from second city Mosul where jihadists launched their offensive late on Monday.
Witnesses said the militants had arrived in trucks mounted with machineguns, while a policeman said his unit was battling them at the northwest entrance to Samarra.
They have since overrun all of Nineveh province and its capital Mosul as well as parts of Kirkuk to its southeast and Salaheddin to its south.
Militants seized Salaheddin provincial capital Tikrit earlier today, and witnesses subsequently said gunmen were also in full control of the Dur and Oja areas between it and Samarra.