Their boat was attacked on the Shatt al Arab river, the ministry said in a statement which gave no further details.
A military spokesman told the BBC that the patrol was caught in an explosion caused by an improvised bomb.
''The use of improvised explosive devices is very common in Iraq,'' said Captain Tane Dunlop, the Multi-National forces spokesman in south Iraq. ''It is slightly unusual in that this time it was targeting a boat.'' Britain has some 7,000 troops in southern Iraq, which has generally been calmer than the centre and north of the country.
More than 120 British armed forces personnel have died in Iraq since the U.S.-led invasion in 2003.
Reuters DKA RS2326