It adds that Mr Cameron's plans threaten to "scupper plans for a new group" for the Conservatives to join after the party's planned withdrawal from the centre-right EPP-ED group after the 2009 elections.
The memo also argues that the legal basis of the proposed sanctions is "very shaky".
But a Conservative spokesman said: "There will always be some people who do not like the new code of conduct but David Cameron has been very clear on the need for transparency and openness with expenses."
The party insists it is determined to take on MEPs who refuse to abide by the changes - but critics say the reforms will only be compulsory for those Tory MEPs planning to fight next year's European elections.
Earlier, Mr Cameron said his proposed code would be stricter than that which applied to other parties' MEPs.
He said it was "unacceptable" for MEPs to be able to make claims without anyone knowing what they were for.
"It's not a pose," he told reporters, adding: "I'm genuinely trying to sort this out".
Under the plans, which come into effect in September, Tory MEPs will have to publish the names of any relatives they employ, their approximate salary and details of any other staff members paid from public funds.
Twice a year, they will be required to publish a breakdown of their expenditure under European Parliament allowances. Anyone wanting to stand as a Tory MEP will have to sign up to the rules.
Mr Cameron said: "I think everybody knows it is time for a deep clean. I believe these changes will help to ensure that the delegation of British Conservative MEPs are committed and, importantly, are seen to be committed to high standards of propriety in public life."
He added: "I don't pretend that any party is whiter than white or purer than pure, but my job with our MEPs is to sort our own stuff out and that is what we're doing."
Mr Cameron said the "vast majority" of the party's MEPs would sign up but that some of those plan to step down at next June's elections may choose not to.
European Parliament investigations into the former Tory leader in Brussels, Giles Chichester, and chief whip Den Dover should be allowed to take their course, he said, although he indicated he was ready to take action if wrongdoing was uncovered.
Bonuses paid to MEPs' staff will be limited to 15% of their annual salary and MEPs will have to confirm that they have repaid any surpluses from their upfront allowances to the European Parliament.
In April, the Tories announced that their MEPs would have to declare whom they employ, whether they are related to them and how much they are paid, within £10,000.
They were also told they would have to publish an annual statement of expenses and travel allowances which will have to be checked by an independent accountant.
The current Conservative leader in Brussels, Philip Bushell-Matthews, told the BBC: "There is no problem. Nobody has said to me that they are not signing this."
Mr Chichester stepped down as the Tories' leader in Brussels after paying thousands of pounds in staff allowances to a firm of which he is a paid director.
The MEP for South West England and Gibraltar said he had not realised the European Parliament's rules had changed and vowed to clear his name.
Under the new rules, Conservative MEPs will no longer be allowed to use so-called service companies to handle the employment of staff members.
From the end of this financial year, they will be required to provide an independent accountant with an annual statement of expenses, including a summary of amounts claimed and how they were spent.
But Mr Cameron said there would be no requirement to provide receipts for every piece of expenditure, as at Westminster.
The leader of Labour's MEPs, Gary Titley, said: "Finally, after eight years, the Tory Party has caught up with the Labour MEPs' regime for dealing with expenses."
Liberal Democrat MP Norman Baker told the BBC: "The reality is that Tory MEPs are a by-word for inappropriate claiming of expenses. The words 'Tory and sleaze' go together as easily as cheese and sandwich."
UKIP Leader Nigel Farage said Mr Cameron's proposals were "more a whitewash than a 'deep clean'".
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