Hawzah News Agency (Cardiff, Wales) - Witnesses reportedly said there were up to four men involved in the alleged attack.
Posted pictures from the scene on Twitter, Yusuf Khan wrote: "Witnesses have said four men ran in to the mosque with knives but I cannot confirm."
Police are still at the scene, which they describe as a "serious incident".
Roads have been closed and buses are diverted, with nearby Cathays rail station also closed.
Dar Ul Isra Mosque said the raid happened in the early hours this morning.
It said: "An incident took place at 1:30am on Sunday 2nd June at Dar Ul Isra community centre in Cardiff.
"Nobody from the mosque was injured and the police have arrested the two individuals who were involved."
"The police are now dealing with this situation and continuing their investigations."
"We thanks South Wales Police for their swift response."