Scotland would be denied access to the UK's most sophisticated and secret intelligence and counterterrorism tools if it became independent, the home secretary, Theresa May, has warned.

She said intelligence-sharing and joint security operations would continue if Scotland became a separate state, but the "seamless, automatic and natural" collaboration which now exists across the UK would become slower and more tightly controlled.

At worst, Scotland would be prevented from taking part in some hi-tech UK government projects, including its £860m cybersecurity programme, and the UK's intelligence-sharing alliance with the US, Canada, Australia and New Zealand, known as Five Eyes.

Scotland would need to prove itself before being allowed to share in that high-level intelligence, by building up its own spying and intelligence infrastructure and offering the five countries a "unique contribution" she said.

May, speaking as the Home Office published the latest UK government analysis paper on the implications of independence, said Scotland would lose automatic access to MI5, MI6, GCHQ and the new National Crime Agency.

She claimed that would damage Scotland's capacity to detect and prevent terrorism, tackle organised and cross-border crime and defend itself against cybercrime.

May said: "If Scotland were a separate state I would expect there to be co-operation between the UK and Scotland, but that would be different from the arrangements we have today. Those arrangements, crucially, is that natural working together, that automatic access to capabilities [which] would not necessary be there in the future were it a separate state."

The Home Office report stated: "The continuing UK would not be in a position to protect Scottish interests as it does presently. Scotland would be a separate state. It could not 'share' the UK's security and intelligence agencies for reasons of sovereignty and democratic accountability.

"An independent Scottish state may not have the capabilities equivalent to those enjoyed by the UK, leaving the Scottish people exposed to greater risks from these national security threats."

The document said Scotland had been attacked by Islamist terrorists, pointing to the Glasgow airport attack in 2007, and Scottish oil workers were caught up in the In Amenas oil refinery attack in Algeria last January.

In Denmark, in 2010, a terror attack on a newspaper was thwarted; Norway suffered from "extreme right wing ideology", the report said, when 77 people were killed by Anders Breivik in July 2011.

Businesses across the UK were also regularly threatened by cyber-attacks, while a new Scottish border would stop Scottish and UK police from "hot pursuit" of criminals fleeing over the border, the report said, and cross-border arrest and search warrants would be slower and more bureaucratic.

May deflected suggestions that the international controversy over revelations about spying and mass data gathering by the UK's secret communications agency GCHQ and the US National Security Agency could strengthen the case for Scotland building a new, independent intelligence capability.

The controversy over the leaks by the former NSA contractor Edward Snowden has escalated sharply in Europe, after allegations that the NSA has been tapping phone calls by the German chancellor, Angela Merkel, and monitoring millions of calls in Spain.

May refused to be drawn on whether that political fallout could influence the independence debate, in the same way the invasion of Iraq or Trident nuclear weapons have done.

She indicated instead that an independent Scotland would be confronted with a choice of whether or not to closely mirror the UK's intelligence-gathering technologies if it wanted effective security.

"What's important for the government of any state which is looking at setting up its security arrangements is that it sets up security arrangements which would be effective and would do the job which is necessary," she said.

"And we have in the UK at the moment effective security and intelligence agencies which are available to the advantage of people across the whole of the UK, including Scotland."

She said an independent Scotland would not be allowed to cherrypick which of that intelligence it liked or did not like if it wanted close and serious collaboration with the UK in the future: it would have no say in what techniques the UK used.

Post-independence, there would be cross-border co-operation "but obviously Scotland would be working with and operating with the UK in the manner in which the UK was undertaking its security operations".

The Scottish government has yet to publish detailed plans and budgets for a post-independence intelligence service, but has insisted it can afford to create new security and defence forces within an annual budget of £2.5bn.

May was highly sceptical about that budget, but said an independent Scotland could not assume that simply by being independent and no longer linked to the UK's foreign policies it would not be at risk of terrorist attack or cybercrime.

It would not necessarily have fewer enemies than the UK, she warned. "There are a number of issues which give rise to the threat which are currently faced by the UK: there are those for whom it isn't country specific, because of foreign policy. There's an issue about the west and the way of life in the west," she said.

"You can't sit here in Scotland today and say definitely the threat would be different if Scotland were a separate state. You can't say the threat would definitely diminish."

Kenny MacAskill, the Scottish justice secretary, did not deal with any of May's specific comments in detail but said the home secretary's claims were wrong. He did not say how an independent Scotland would organise its intelligence and security services but said Scotland already had an independent police and justice system that was fully able to handle internal terrorism issues, and which worked closely with other UK forces.

"An independent Scotland will have first rate security arrangements to counter any threats we may face. And we will continue to work in very close collaboration with the rest of the UK and international partners on security and intelligence matters, which is in everyone's interests," he said.