The crisis facing the defence secretary, Liam Fox, over his links to his self-styled adviser and friend, Adam Werritty, has deepened after it emerged that Werritty ran a controversial charity from inside Fox's office in the houses of parliament.

The Guardian has established that Werritty used Fox's room 341 in the MPs' block at Portcullis House as the official headquarters of a rightwing charity, the Atlantic Bridge, which works in conjunction with a major US business lobby group. The office was provided to Fox at taxpayers' expense while he was in opposition until last year.

It also emerged that between 2007 and 2010, Werritty earned more than £90,000 as chief executive of the Atlantic Bridge, and that the most senior civil servant in the Ministry of Defence had warned Fox about his connections to Werritty. Ursula Brennan, permanent secretary at the Ministry of Defence, told Fox to stop Werritty handing out business cards embossed with parliament's portcullis logo that describe him as an "adviser to the Rt Hon Dr Fox MP".

Pressure has been growing all week on the defence secretary to explain his links with 34-year-old Werritty, who was Fox's best man and former flat mate. Werritty is not a government employee and has not had security vetting, but has visited Fox at the MoD offices in Whitehall 14 times in a little over a year, and joined Fox on an official ministerial visit to Sri Lanka this summer. He also brokered a meeting for the defence secretary in Dubai in June that may lead to Fox being called to give evidence in a blackmail trial in the US.

Company records have shown that Fox was previously an investor, alongside Werritty, in a healthcare consultancy firm, UK Health.

Fox arrived in Libya on Friday evening and was reported to have met with Jalal al-Digheily, who is defence minister in the National Transitional Council interim government. He was greeted at the airport in Tripoli by British envoy John Jenkins.

The shadow defence secretary, Jim Murphy, said the growing evidence about Fox's relationship with Werritty amounted to "a crisis engulfing the defence secretary".

"We need a thorough official investigation, but it is not good enough to use that as an excuse for silence," Murphy said. "There are multiple questions that deserve specific answers, which Liam Fox should provide now. This matter is overshadowing the important work of the Ministry of Defence and only Liam Fox himself can put it to rest."

On Thursday, Fox asked Brennan to launch an investigation into what he called "wild allegations". On Friday, he said it was "unacceptable" that Werritty had distributed the business cards. "I understand those cards are no longer used. I have made it very clear to him that it's unacceptable to carry a card saying that he is a personal adviser."

Fox has previously been criticised for using a US aide with links the US intelligence service and army as an adviser at the MoD before he received full security clearance.

Fox founded the Atlantic Bridge to strengthen the relationship between the US and UK, and in particular celebrate the Reagan-Thatcher era. He installed Werritty as chief executive, but it has now been wound up following criticism by regulators that it was too political to qualify for charitable status.

A string of senior Tories, including George Osborne, William Hague and Michael Gove, have served on the advisory board of the charity, and Baroness Thatcher was the honorary patron.

Fox's parliamentary office was given as the charity's administrative office in UK charity files, and Werritty is listed as UK executive director in accounts filed in the US for the Atlantic Bridge Inc, the entity which controls the organisation's US arm.

One parliamentary staff member, whose office was close to Fox's, said he believed that Werritty may have held a parliamentary pass. "I assumed he was a member of Fox's staff because he was always around," the official said.

The parliamentary commissioner for standards' office, that oversees the list of pass holders, could not verify the claim.

A spokesman for Fox insisted Werritty was rarely in the office, although it was manned by an administrator for the charity.

The presence of the charity's administrative office at the heart of parliament also exposed Fox's potentially embarrassing links to US neo-conservative lobbyists whose views on the environment and public healthcare clash with the stated policies of David Cameron's government.

In 2007, the American Legislative Exchange Council (Alec), a major US lobbying organisation for big corporations thought to include Philip Morris, Texaco and McDonalds, set up a sister charity also known as Atlantic Bridge, which then funded Fox's organisation with £28,528 over the past four years, accounts show.

Alec did not answer enquiries about whether it funded the charity, but it has described it as "the latest component of its international relations programme" and appointed its director of international relations, Catherine Bray, to run it.

Werritty is listed in US charity files as the American arm's UK executive director, and his address is given as Fox's former room at the House of Commons.

Alec announced the formation of the charity in October 2007 "in conjunction with the Atlantic Bridge Group, a non-profit organization chaired by the British Conservative shadow minister for defense, Liam Fox MP".

As well as 300 corporate members, Alec has 2,000 state legislators as members, and a goal of the combined project was to substantially increase its number of European legislative members.

Its slogan is: "Limited government, free market, federalism".

It sparked a transatlantic row when John Campbell, a California congressman and an active member of Alec, attacked the NHS as "enormously inefficient, wasteful and costly" and said it was "nuts" of President Obama to seek to emulate it in his healthcare reforms.

Alec has also fought cap-and-trade programmes and other regulations of greenhouse gases on behalf of big business, and has attacked attempts by the Environmental Protection Agency to introduce new rules on air and water pollution as "a regulatory train wreck".