A group of computer hackers claimed responsibility for what appeared to be a denial of service attack last night, which left users unable to fully access the department's homepage for several hours.
A message on the site said the page was unavailable “due to a high volume of traffic”.
One message on Twitter claiming to be from Anonymous, a loosely organised group of hackers, said the action was “for your draconian surveillance proposals”, while another said it was in protest at the UK's controversial extradition treaty with America.
It read: “You should not give UK citizens to foreign countries without evidence. If an offence happened in the UK, so should the trial.”
Another tweet claiming to be from members said the action had been taken in “protest of the potential extradition of Gary McKinnon, Christopher Harold Tappin & Richard O'Dwyer.”
A Home Office spokeswoman said tonight: “The Home Office website was the subject of on online protest last night.
“This is a public facing website and no sensitive information is held on it. There is no indication that the site was hacked and other Home Office systems were not affected.
“Measures put in place to protect the website meant that members of the public were unable to access the site intermittently.
“We will continue to monitor the situation and take measures accordingly.”
There were also claims on Twitter that Anonymous had disrupted the websites of the Ministry of Justice and Number 10.
One message said: “£Anonymous launched a cyberattack on http://www.number10.gov.uk, http://www.homeoffice.gov.uk & http://www.justice.gov.uk resulting in multiple TANGO DOWNS.”
All three Government websites were fully operational today however.
A later Anonymous tweet read: “Why TANGO DOWN the UK govt? Proposed draconian surveillance measures in combination with continued derogation of civil liberties.”
A denial of service attack prevents a website from functioning properly, sometimes by swamping it with more traffic than it can handle.
The cyber protest came after it emerged last week that the Government was planning a massive expansion of its powers to monitor the email exchanges and website visits of every person in the UK.
Under legislation expected in next month's Queen's Speech, internet companies will be instructed to install hardware enabling GCHQ - the Government's electronic “listening” agency - to examine “on demand” any phone call made, text message and email sent, and website accessed, in “real time” without a warrant.
The Government has faced strong opposition to the plans, with senior Conservatives joining Liberal Democrats and civil rights campaigners in warning they would cause a gross intrusion into freedom and privacy.
Lib Dem president Tim Farron vowed the party would “kill” proposals for increased monitoring of emails and internet use if they were not watered down.
He told BBC1's Andrew Marr Show he was prepared to look at draft legislation, dubbed a “snoopers charter”, when it is published but warned he was “in no mood” to back “authoritarian” laws.
He said many Lib Dems were “horrified” by the plans.
But Home Secretary Theresa May defended the proposals, telling the Sunday Telegraph: “I would hope that we will be able to do this in a Bill in the next session, but in a way that enables people to have a sight of the clauses.”
Meanwhile, the House of Commons Home Affairs Select Committee has called for an overhaul of the controversial extradition arrangements between the UK and the United States to restore “public faith”.
Many critics believe it is easier to extradite a British citizen to the USA than vice-versa.
Retired British businessman and all-Kent Golf Club Union president Tappin, 65, is being held in jail in New Mexico while he awaits trial on arms dealing charges after being extradited last month.
Student Richard O'Dwyer, 23, of Chesterfield, is also fighting extradition after being accused of breaking American copyright laws by using his computer in the UK.
And Asperger's sufferer Gary McKinnon, 46, from Wood Green, north London, is still waiting to hear whether he will be extradited over charges he hacked into US military computers 10 years ago.
Anonymous, whose genesis can be traced back to a popular US image messaging board, has become increasingly politicised amid a global clampdown on music piracy and the international controversy over the whistleblowing website WikiLeaks, with which many of its supporters identify.
Authorities in Europe, North America and elsewhere have made dozens of arrests, and Anonymous has increasingly attacked law enforcement, military and intelligence-linked targets in retaliation.
One of Anonymous's most spectacular coups was secretly recording a conference call between US and British cyber-investigators tasked with bringing the group to justice.
The collective has no real membership structure, with hackers, activists, and supporters able to claim allegiance to its freewheeling principles at their convenience.