Theresa May’s appeal for a special Brexit deal on science and research collaboration, worth billions to the British economy, is being stonewalled by Brussels as it prepares to offer an arrangement less privileged and more expensive than that given to non-EU states such as Israel.

The European commission’s negotiators refused to discuss the issue in formal talks last week, instead insisting they would present the UK with conditions of entry for a “third country” into its €97.9bn research programme once they had been formally published.

A draft copy of the so-called Horizon Europe document, seen by the Guardian, suggests that the UK is set to be offered less generous access than countries with associate status in the current programme, known as Horizon 2020, including Israel, Turkey, Albania and Ukraine.

Those states, along with countries in the European Free Trade Association (EFTA) – Iceland, Liechtenstein, Norway and Switzerland – will be “associated to all programme parts” of the new research and science framework, details of which are to be published on 7 June, according to the leaked document.

It is understood that wealthy countries with a developed research and development capacity are to be offered a greater opportunity to pay in and collaborate with the EU under a reform of the current programme, which will end in 2020.

However, the UK is set to join Canada and South Korea in the category of countries that will have to pay a higher price for the privilege of collaborating, while being barred from a particular raft of programmes designed to encourage innovation.

According to the draft paper, so-called “third countries” will not have a seat on the new European Innovation Council, which sets priorities, and their companies will not have the opportunity to apply for “fast, flexible grants and co-investments” designed to “bridge the ‘valley of death’ between research, commercialisation and the scaling-up of companies”.

Sources said it was additionally unclear what role the UK would have in shaping the priorities of Horizon Europe after Brexit, given it would no longer be a member state and would not be an EFTA member, acceding country, candidate country or potential candidate country.

The European commission’s proposals will need to be approved by the member states. A senior EU official said they were aware that the UK would seek to change the rules from within during negotiations over the bloc’s future budget, known as the multi-annual financial framework (MFF).

An EU official involved in the Brexit negotiations said of last week’s talks with the UK negotiators in Brussels: “We … had a discussion on science and technology where we said that from our point of view unfortunately this was slightly early as we are coming forward in early June with the proposals for the next generation of Horizon Europe, the successor to Horizon 2020, and these programmes will set out the conditions for third countries’ participation.

“We would be happy to present that to the UK once that has been published. We take good note that the UK wants to maintain its role in shaping and priority setting of EU programmes in the future, and we also took very careful note of the announcement by the UK negotiators that they intend to use their part in the EU28 negotiations about the future MFF as an instrument to influence the definition of third country part rules in EU programmes.”

A UK paper published earlier this year noted that the country’s research institutions had been awarded 15% of all agreed funds under Horizon 2020, worth about €4bn (£3.5bn).

Last week a British presentation to the EU negotiators, who were led by Michel Barnier, argued for full access to Horizon Europe and said “as an associate country we would look to agree an appropriate level of influence on the shape of the programme. This should be greater than current non-EU precedents, recognising the quality and breadth of the UK’s contribution”.

Thomas Jørgensen, the senior policy coordinator at the European University Association (EUA) working on Brexit-related issues, said the commission was acting to protect its interests in the face of the emergence of the UK as a rival economic power.

He said: “It is entirely understandable that you would want to help small countries in your neighbourhood, but why would you do that for small and medium-size enterprises in South Korea or other third countries such as the UK?

“The view from Brussels is that leaving the EU is the UK’s choice, it is their choice to be South Korea. If they say they want a special deal, that’s not going to work.”

Jørgensen said, however, that the scale of the UK’s research strength was such that it would inevitably have a large say in at least informal settings about the direction of the programmes.

He said: “There is elasticity. But if it comes down to a matter of principles, then that could be a problem.”

Diplomats attached to the member states suggested there were additional concerns about giving third countries access to sensitive research information. The UK is seeking an agreement to continue the flow of data between it and the rest of Europe, but a recent report on the country’s handling of personal information held on the Schengen Information System, designed to monitor the flow of people around Europe, has damaged that case.

An official paper, dated 18 May 2018 and seen by the Guardian, reveals that despite a 2015 evaluation finding serious deficiencies with the UK’s handling of personal data, a follow-up visit in 2017 had discovered that a range of recommendations had not been implemented.

The report notes that the EU’s inspectors had found that “very serious deficiencies in the legal, operational and technical implementation of SIS by the UK subsist”.

Among the issues that caused concern was the discovery that UK officials had been copying personal data and sharing it with US contractors working for its immigration services and the border police. Some of that information was found to be out of date as well, raising the potential of people being unfairly flagged as they passed through the UK’s borders.

In a further indication of the EU’s attitude, on Wednesday the commission announced that the UK could take part in the student exchange scheme, Erasmus, after Brexit, in return for a financial contribution, but that it would have no say in shaping the programme.