Two prominent scientists are refusing to allow their work to be included in the Science Museum’s collection because of the institution’s links to Shell.

Steve and Dee Allen, who have carried out some of the most important research into global plastic pollution, say the museum’s sponsorship deal with the fossil fuel company – and a subsequent “gagging clause” – meant it was no longer a credible scientific institution.

“They have positioned themselves to fail in both of their primary tasks – to preserve and present the truth as best we know it,” said Steve Allen.

The decision by eminent scientists to boycott the museum is the latest blow to the institution, which has had several resignations and faced growing protests over its relationship with Shell – and a newly announced deal with the “green” arm of the global fossil fuel corporation Adani.

The Science Museum rejected the academics’ claims, saying that including an item in its national collection was “a significant process” and in this case “none of those formal steps towards an acquisition had been initiated”.

A museum spokesperson also rejected the claim its sponsorship deal with Shell had any impact on its independence.

“We entirely reject the false allegation that our curators are in any way inhibited in carrying out their vital role in an expert, independent and thorough manner,” a spokesperson added.

The scientists – who are married – said they were approached by the Science Museum and asked if their work could be included in the institution’s archive. Before declining, they said they had several online discussions with the museum, agreeing which items would be suitable and how they would be delivered.

“We stand by our claim that the Science Museum contacted us for items to be placed in the permanent record,” said Dee. “But in the end we declined because we were unhappy with the museum’s relationship with Shell and Adani and its treatment of climate protesters.”

In particular, the scientists were concerned with a clause in its contract with Shell that prevents the museum from “damaging the goodwill or reputation” of the oil giant.

“One is left to assume the Science Museum is now telling the ‘truth as best we are allowed’,” said Steve Allen.

The scientists’ decision is the latest blow to the institution over its relationship with fossil fuel companies. In October, the leading climate scientist professor Chris Rapley, a former director of the Science Museum, resigned from its advisory board saying he disagreed with its “ongoing willingness to accept oil and gas company sponsorship”.

Later that month, two trustees – Hannah Fry, a professor in the mathematics of cities at University College London, and Jo Foster, the director of the UK charity the Institute for Research in Schools – resigned from the museum’s board in protest at its deal with Adani.

Fry said the Science Museum was “giving the false impression that scientists believe the current efforts of fossil fuel companies are sufficient to avoid disaster”.

There have also been several protests at the museum, most recently when youth activists occupied it overnight.

The Allens said they were initially honoured to be asked for their work – which has included pivotal studies into the extent and impact of plastic pollution – in the museum’s archive, but added that when they looked into its relationships with fossil fuel companies they felt they could not go ahead.

“We felt that their impartiality has been compromised,” said Steve Allen. He dismissed the Science Museum’s claim that no formal offer to include their work had been made.

“It really doesn’t matter what they say, it only matters how their actions are perceived by us in the scientific community, and the public. We have lost confidence in the Science Museum.”