Since 14 June, registering patients have been required to sign a 'counter-fraud declaration' that permits their details to be shared with around eight agencies, including the UK Border Agency, the Department for Work and Pensions and HM Revenue and Customs.
The Scottish government said the move was part of a wider rolling programme of counter-fraud measures.
A spokeswoman said it will safeguard the NHS from people who look to abuse the system to obtain services they are not entitled to free of charge.
'If a patient is in need of emergency treatment they can still be treated by GPs as a temporary resident,' she added.
But Dr John Ip, medical secretary of Glasgow LMC, warned the new form could put people off registering at practices.
This could mean people miss out on medical treatment, and children missing screenings and vaccinations.
Dr Ip said: 'My concern is that GP practices have always been promoted as confidential, but on the back of this form it is fairly blatant that certain information will be shared with all types of organisations.
'It is a fairly sledgehammer declaration hammering home the message that the government is watching all of us.
When people are vulnerable and seeking medical help this is probably unhelpful.'
A spokeswoman for BMA Scotland said it is not the duty of GPs to police the system.
She said: 'We would be concerned if people avoided seeking medical care for themselves or their children because they are reluctant to have their information shared with various government agencies.
'It is important that patients who are entitled to NHS care have a right to choose not to sign up to this.'
The amendment to registration forms has only been implemented in Scotland, the spokeswoman confirmed.