The home secretary, Sajid Javid, has been warned by Brussels that the UK’s own nationals will suffer if it introduces a post-Brexit immigration system that discriminates between European citizens according to their skills.

The policy is likely to be unveiled at the Conservative party conference, which begins on Sunday.

Following a meeting this week with the prime minister and Javid in Whitehall, Guy Verhofstadt, who represents the European parliament in the Brexit negotiations, has – in a letter obtained by the Guardian – given warning of a tit-for-tat response.

Verhofstadt, a former prime minister of Belgium, tells Javid that any discrimination among EU nationals on the basis of nationality or employment “would apply reciprocally to UK citizens moving to the EU 26”. By EU 26 he means all the the member states excluding Ireland, which is in a common travel area with the UK. The conclusion is understood to be supported by EU officials and diplomats representing the member states.

Theresa May’s cabinet agreed in principle on Monday that EU citizens should face the same immigration rules as people from the rest of the world if they want to live or work in the UK. The cabinet decided that “skills, not nationality” would be the test for people seeking to move to the UK.

Such a system would most likely be phased in after the 21-month transition period, during which the UK will abide by EU rules, including the free movement of people.

The decision is likely to be trumpeted at the Tory conference in Birmingham, with May keen to find some positive Brexit news to cheer her party members.

In his letter to Javid, Verhofstadt, who leads a cross-party Brexit steering group of MEPs, writes: “We know this matter was discussed in cabinet on Monday and that it will be the subject of a further white paper to be issued shortly.

“We await to see the details of that white paper on what will be an important element of a future EU-UK association agreement.

“The [European parliament’s Brexit steering group’s] initial thinking on this was that while we would be open to a variety of different mobility arrangements, it would be difficult for the parliament to agree to arrangements that were discriminatory in terms of nationality or type of employment.

“It was also our strong view that whatever was finally agreed with respect to EU citizens wishing to move to the UK would apply reciprocally to UK citizens moving to the EU 26.”

The issue of citizens’ rights has been the central preoccupation of the European parliament, which will have a right to veto any withdrawal agreement struck between the UK and the EU.

Verhofstadt also calls for the British government to spell out its thinking on the right of onward movement for EU nationals who are given settled status in the UK. As it stands, those with such rights to stay would lose them if they left the UK for five years or more.

Verhofstadt writes that should the UK revise its position and adopt “a lifelong right to return” it may then be possible for the EU to allow British nationals living in one member state before the end of the transition period to move on to live in another member state.

In his letter, Verhofstadt also updates Javid on the plans of the member states with regard to how they will give settled status to British nationals who had moved to the continent before the end of the transition period.

The UK has adopted an application system under which the 3 million EU nationals in Britain can apply through an app requiring personal data, a scan of a passport, address, email address and a selfie to match the passport picture.

The system then matches the biographical details with HM Revenue & Customs records to give applicants an instant answer as to whether their applications have been successful.

Verhofstadt tells Javid that 15 member states have also decided to take this approach to giving settled status to the British nationals living in their countries.

Ten member states, he writes, have opted for a simpler, declaratory approach, favoured by the lobby groups representing EU and British nationals most affected by Brexit, under which they can assume settled status and “which means very little change as to the situation today”. The EU is also looking at providing an identical set of papers to all British nationals with settled status.

Verhofstadt writes: “There is large consensus among member states on the need to have uniform documentation for UK citizens allowing easier recognition across the EU. There are, however, diverging approaches regarding the dates from which it will be possible to submit applications and for the start of the accompanying information campaigns.”