Their boat was attacked on the Shatt al Arab river on Sunday, the ministry said in a statement. The routine patrol was caught in an explosion caused by an improvised bomb, a spokesman said.
The ministry spokesman said: "The patrol was subject to an improvised explosive device."
Captain Tane Dunlop, the multi-national forces spokesman in southern Iraq, told the BBC: "The use of improvised explosive devices is very common in 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, and 125 British armed forces personnel have died since the US-led invasion in 2003.
The latest deaths will add to pressure on Tony Blair, the British prime minister.
Three US soldiers died on Saturday from wounds suffered in combat in the western Anbar province, the US military said.
Bush is pondering a shift in tactics in Iraq after his Republican party's defeat in last week's mid-term elections.
Bush and Blair, whose popularity has also collapsed because of the war, are seeking ways to stop attacks by fighters and gradually draw down their troops.
Bush will speak on Monday to a bipartisan US panel that is seeking alternative strategies for Iraq and Blair will give evidence to the same panel via videolink on Tuesday.
The latest deaths came on the day thousands of British veterans and military personnel around the world remembered the nation's war dead at dozens of Remembrance Sunday services.
"This terrible incident reinforces in our minds the sacrifice made by the brave men and women of our armed forces," Des Browne, the British defence minister said in a statement.