In a statement published on Saturday, Downing Street said there was "no suggestion that Mr. Harper knowingly employed an illegal immigrant," adding that Prime Minister David Cameron had "accepted his resignation with regret."
Harper launched a campaign last year aiming at intimidating undocumented foreign immigrants with portable billboards to "go home or face arrest."
In his resignation letter, Harper wrote that he had verified the cleaner's passport and documentation in 2007 and had not broken the law; however, he believed that his position required “a higher standard than expected of others."
"Although I complied with the law at all times, I consider that as immigration minister, who is taking legislation through Parliament which will toughen up our immigration laws, I should hold myself to a higher standard than expected of others," he said in the letter.
He also added that immigration officials warned him about the illegal cleaner on Thursday morning.
"I immediately notified the home secretary and my permanent secretary. This is now a matter for immigration enforcement," he wrote.
Regarding Harper’s viewpoint, Cameron said, "I understand your view that, although you carried out checks on your cleaner, you feel that you should hold yourself to an especially high standard as immigration minister."
Harper's resignation is embarrassing for the UK government because he was specifically responsible for the administration’s immigration policies, which are increasingly tightening.