Weapons exported to South Sudan in a deal allegedly brokered by a British company could be used against UK troops who have been deployed to the war-torn country as part of a UN mission, Amnesty International has warned.

The Department for International Trade is investigating whether the deal, which has been brought to light by Amnesty International, constitutes a breach of British arms export controls.

An EU arms embargo has been in force against South Sudan since its independence in 2011, while Britain has been one of the leading proponents for the establishment of a UN arms embargo.

However, documents leaked to Amnesty name a British company registered to an address near Covent Garden in London, S-Profit Ltd, as being among the commercial players in what would constitute one of the largest single arms deals that South Sudan has entered into since the outbreak of major civil conflict in December 2013.

In response to Amnesty’s claims, S-Profit’s director denied that the company has supplied military product to South Sudan but was silent on whether it had played any kind of intermediary role.

The weapons form part of a previously undisclosed 2014 contract between a Ukrainian state arms company and a UAE-based company to procure $169m (£126m) of weapons on behalf of the South Sudanese government. These include thousands of machine guns, mortars, rocket-propelled grenades and millions of rounds of ammunition.

Amnesty claims that the involvement of a British company in such a deal could violate UK export controls that prohibit involvement in the supply of weapons to South Sudan, where the conflict is now in its fourth year with about 3.8 million people having been driven from their homes. The violence was described earlier this year by the international development secretary, Priti Patel, as genocide.

Oliver Feeley-Sprague, programme director for Amnesty UK’s work on arms controls, said: “It is undeniable that huge arms deals such as these are also a direct threat to the lives of hundreds of UK troops that are currently in South Sudan as part of UN peacekeeping operations. Is the UK seriously going to wait until British blood is spilled before it takes proper action to stop dodgy companies brokering arms deals on UK soil?”

A spokesman at the Department of International Trade said: “We are aware of the allegations made by Amnesty and are currently investigating whether there have been any breaches of our export controls system.

“The UK has one of the most transparent and accessible company registers in the world – viewed 2 billion times last year – meaning company information is under constant scrutiny. When irregularities are identified, Companies House takes action and if necessary alerts the relevant law enforcement agencies.”

Companies House, the UK government body responsible for registering companies, declined to comment on the case. However, in response to questions from Amnesty about the activities of S-Profit and UK company registration procedures, the authority’s acting chief executive said that it “carries out a number of checks on all information received, ensuring it is valid, complete, correctly formatted and in compliance with company filing requirements ... The obligation to ensure the information is accurate lies with the company and its directors.”

Ann Lewis insisted that Companies House’s policy of making company documents public was adequate to prevent “false, inaccurate or possibly fraudulent information” since it allowed “civil society groups” to “highlight patterns, errors and erroneous information”.