There have been no reports of casualties.
"A group of armed men attacked the mausoleum of Imam Ali al-Hadi at 7am, neutralised the policemen guarding the building before placing two explosives charges and blowing them up," police said.
Local residents said the two explosions brought down part of the dome of the al Askariya shrine, but there were no reports of injuries.
The mausoleum to the 10th Shiite imam in the town, 125 kilometres north of Baghdad, is an important pilgrimage centre for Shiites.
It contains the tombs of two revered Shiite imams.
The head of the Sunni religious endowment organisation, Ahmad Abdel Ghaffur al-Samarrai, immediately condemned the attack, terming it "a criminal act".
Religious leaders at other mosques and shrines throughout Samarra also denounced the attack, in statements read over loudspeakers from minarets.
It is feared the attack will further raise tensions between the majority Shiite and minority Sunni communities in Iraq, as political factions bicker over the formation of a national unity government.
Meanwhile, a roadside bomb near a primary school in a mostly Shiite area in Kut, southern Iraq, has killed two boys and injured four others.