The IPO said that it had been a victim of Operation Payback, the series of co-ordinated online attacks on organisations related to the enforcement of copyright law.
The whole IPO website was taken offline on Saturday and only a limited online service has been restored, a spokesman said.
"The Intellectual Property Office chose to disconnect its website from the Internet following a coordinated Distributed Denial of Service (DDoS) attack on Saturday 16th of October at around 18:00 BST," said an IPO statement. "As part of our standard network security procedures, our main services were protected prior to the attack. The website and our internal services suffered no harm."
Operation Payback has already attacked the websites of US film industry trade body the Motion Picture Association of America, Kiss singer Gene Simmons and others.
It was behind the attack on UK law firm ACS Law, which had sent letters threatening legal action against people accused of downloading copyrighted material. When the law firm was putting its website back online it accidentally published its email archive, exposing the personal details of the accused individuals to the web and causing a privacy outcry.
A statement attributed to the group behind the attacks, which is known as Anonymous, said that copyright law is censorship.
"History repeats itself," it said. "There was a time when powers that be attempted to silence the printing press, the blank cassette and the recordable CD. All of these previous attempts at censorship have failed, and future attempts of this nature are doomed to failure."
The IPO said that its trade mark and patents filing systems were not yet online but that filings could be made by post, fax or by hand at its offices in London and Newport. It said that systems based on software run by the European Patent Office are working.
A distributed denial of service (DDoS) attack overloads web servers with a deluge of automated requests to see a web page, blocking access to it from non-automated sources, such as normal visitors.
"The organisers say that they have targeted us as we are 'perpetuating the system which is allowing the exploitative usage of copyrights and intellectual property'," said the IPO statement.
A statement sent to users of its services said that the IPO is "continuing to monitor the situation and assess the risks. We are also considering our security options for the longer term."
