It has drawn up a confidential “warnings index” of people from the two states, most of whom are suspected of having criminal associations or posing a security risk.

According to a paper circulated in Whitehall last week, ministers fear they may be unable to stop these people settling in Britain and claiming state benefits when Romania and Bulgaria join the EU.

The paper reveals that the government privately estimates between 60,000 and 140,000 Romanians and Bulgarians will arrive in Britain in the first year after accession.

Ministers were criticised for underestimating the number of migrants from the eight eastern European countries that joined the EU in 2004. Experts last week revealed that 600,000 had come to Britain since 2004, compared with the government’s estimate of between 5,000 and 13,000 a year.

The Home Office paper, from Joan Ryan, the Home Office minister, reveals deep concerns in government that a new wave of immigration may provoke a public backlash.

It warns of EU “enlargement fatigue” and that the “enough is enough” argument is winning.

The list of “undesirables” was compiled by the Immigration and Nationality Directorate (IND) and other law enforcement agencies from records of Bulgarians and Romanians who entered or tried to enter Britain.

It includes individuals who have been flagged because of immigration irregularities, passport fraud and links to crime.

The 45,000 figure may, however, be an underestimate because it includes only those people whom the British authorities know about through investigations into organised crime or stolen passports.

Once Bulgaria and Romania, known as the A2, join the EU, Ryan said it would be harder to expel such undesirables or stop them entering Britain.

On July 18, she wrote: “They will enjoy the same rights as other EEA [European Economic Area] nationals, who cannot easily be deported. In the past, A2 nationals have been removed for immigration-related offences which will cease to apply from accession.

“The key to us knowing when A2 criminals seek to enter the UK is to ensure that we have as much information as possible on serious criminals to include on the WI [warning index]. A2 governments can help, but they may want something in return.”

At present, such criminals can be identified and barred from entering Britain through the checks required to obtain a visa. As EU citizens, the only requirement will be to produce a valid passport on entry. As a result, the paper reveals, ministers are considering refusing Bulgarians and Romanians the right to work in Britain.

“The issue is whether we think that the . . . impact of A2 access can be managed . . . or whether the political impact of unlimited A2 access at time of growing public anxiety over immigration means that we should restrict access, despite the operational complexities,” Ryan wrote.

Ryan’s paper reveals the depth of concern about a backlash from the public and media. She says migrants from Bulgaria and Romania will be “more visible” than those from other eastern European countries because unlike the Poles, for example, they have less well established communities here. There are also concerns that these migrants could bring with them organised crime and corruption, which is more established in these two countries.

Ryan suggests it might be unwise to publicise the estimate of up to 140,000 migrants as the government has been previously criticised for underestimating expected numbers of migrants.

She admits there have been areas of “strain” within communities as a result of east European migrants, particularly over housing. The number of east Europeans in UK prisons has trebled since June 2004 to about 560.

John Reid, the home secretary, is to announce plans to double the immigration agency’s budget and make all staff wear special uniforms to provide a visible presence at ports and borders.

MPs will this week fuel the controversy over immigration policy by calling for control over the system to be transferred from the home secretary, John Reid, to a new Cabinet committee.

A report by the Commons home affairs select committee claims the entire system suffers from “fragmentation and lack of communication” and recommends the establishment of an independent Immigration Inspectorate to oversee border control.

The report reveals there were 703 allegations of corruption at the Immigration and Nationality Directorate between 2004 and 2005.

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