The arrests came just hours after police charged three people with public order offences for staging a pro-Palestinian protest outside the London home of opposition leader Keir Starmer.
The incidents come amid debate in Britain over the acceptable limits of public demonstrations, with fears for lawmakers' safety increasing since the start of the war in Gaza.
Protest groups Palestine Action and Youth Demand said their activists had spray-painted the ministry's facade.
"We no longer accept the continuation of this death project as the UK allows the funding of arms to Israel," Youth Demand posted on social media, alongside video of the stunt.
Transport police officers assigned to a central London protest made the five arrests after spotting "a group of people spraying paint on a building along the Embankment," London's Metropolitan Police said.
"We will never tolerate people causing criminal damage to buildings under the guise of protest," the force said on X, formerly Twitter.
Earlier, the Met said two women and a man had been charged under section 42 of the Criminal Justice and Police Act 2001 over the protest Tuesday outside Labour leader Starmer's home.
"This power stops the harassment of a person at their home address if an officer suspects it is causing alarm or distress to the occupant," it added.
The accused, all in their 20s, were arrested outside Starmer's Kentish Town house in north London.
They had hung a banner outside the house reading: "Starmer stop the killing", surrounded by red handprints.
They also laid rows of children's shoes in front of the door to signify children killed in Gaza.
The three are due to appear in court on Wednesday.
Conservative Prime Minister Rishi Sunak, whose home was targeted by environmental protesters last year, has urged police to halt protests outside lawmakers' residences, parliament, and political party offices.
In February, he claimed Britain was descending into "mob rule" in comments that were criticised by civil liberty groups.
UK lawmakers have reported receiving a surge of abuse since Hamas's deadly attack on Israel on October 7.
Earlier this year, Sunak's government announced a package of GBP 31 million ($39 million) towards boosting MPs' security.
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