Allegations that a charity founded by the chief executive of Vote Leave, a group campaigning for Britain to leave the EU, has broken the law by funnelling donations to political groups campaigning for a British exit are being examined by the charity commission.

The Politics and Economics Research Trust (Pert) gave 97% of its grants last year to groups who favour Brexit, according to a letter of complaint sent by a senior Labour MP. Matthew Elliott, the chief executive of Vote Leave, who is also a former chief executive of the Taxpayers’ Alliance, founded Pert in 2004.

Charities are not legally allowed to exist for a political purpose. Of £532,000 the charity paid out in grants in 2014, £300,000 went to the Taxpayers’ Alliance and £205,000 to Business for Britain, both of which are Eurosceptic. £10,000 went to Global Britain, which has campaigned for Brexit. In 2013 the charity gave £415,000 to the Taxpayers’ Alliance and Business for Britain.

Charitable donations, unlike payments direct to Eurosceptic campaigns, may benefit from gift aid, which allows the charity to reclaim tax on a donation made by a UK taxpayer. The Politics and Economics Research Trust claimed more than £58,000 in gift aid in 2013.

Emma Reynolds, a former shadow minister for Europe, is understood to have written to the Charity Commission raising concerns that “Pert may be in breach of charities’ legally binding commitments to preserve their independence, specifically regarding political activity and the delivery of charitable objectives.” She added in her letter: “Given that it appears that Pert has been engaging in day-to-day political activity, can you confirm whether its conduct is in contravention of the law?”

A spokesman for the commission said: “We are aware of concerns concerning the charity the Politics and Economics Research Trust and are currently assessing those concerns to determine what if any regulatory action may be required.”

Moira Protani, lawyer for the charity, denied any wrongdoing on behalf of her client. She said: “My client does not campaign and neither does it have a political ‘agenda’ in its grant-giving activity. It provides funds for the purpose of conducting high-quality research which furthers the charity’s objects.

“My client has built up a relationship with organisations which, in its opinion, have competent researchers capable of conducting an independent analysis on a given subject with rigorous methodologies and processes. Like other charities, my client is entitled to claim gift aid relief on donations from taxpayers where the donations are applied for charitable purposes.

“In practice my client makes grants towards the costs of research which fall within the objects of the charity. My client expects grant applicants to apply rigorous processes and methodology to any research which is conducted and to publish the results of the research.”

Prominent Eurosceptics who have donated to Pert include the Peter Cruddas Foundation, which donated £100,000 in 2011 and £10,000 in 2013. Cruddas, a former Conservative party co-treasurer, is also a financial backer of the Vote Leave group.

In 2011 the charity received a warning from the Charity Commission over the need for it to “properly manage” its relationship with the Taxpayers’ Alliance following a complaint from former deputy prime minister John Prescott.

Prescott filed his complaint after the Guardian reported that one donor, the Midlands Industrial Council, a business pressure group, had been asked to donate money to Pert for use by the Taxpayers’ Alliance, to attract gift aid. The charity commission found no evidence that the Midlands Industrial Council did ultimately make any donation.