US intelligence chief James Clapper has warned potential deep budget cuts could damage morale and undermine the mission of the country's spy agencies, according to a letter obtained by AFP Thursday.

Clapper, America's director of national intelligence, voiced grave concern over plans to impose a furlough on all Defense Department civilian employees if drastic automatic budget cuts enter into force next month.

In his letter to Defense Secretary Leon Panetta, the spy chief said civilians working for spy agencies should be protected in same the way that troops in uniform are being shielded from potential cost-saving measures.

"Let me be clear: I am opposed to implementing uniform furloughs without first considering the potential impact on our mission and national security," Clapper wrote in the February 1 letter.

"We've invested heavily in building a workforce that is second to none, so we can't afford to ignore the adverse implications that furloughs bring in terms of hardship, morale, and inefficiency," he wrote.

"Our ability to perform our mission would be seriously undermined by mandatory across-the-board furloughs."

The Pentagon plans a mandatory 22-day furlough for its civilian workforce in the event Congress fails to reach a budget deal by a March 1 deadline.

By law, without an agreement in Congress on slashing federal spending, multi-billion dollar cuts will be triggered across the government.

Much of the funding for intelligence agencies falls within the Pentagon's budget.

But officials say Clapper has authority over "national intelligence program" funds that pay thousands of employees spread across 16 agencies, including the Defense Intelligence Agency, the National Geospatial-Intelligence Agency and the National Reconnaissance Office.

The release of the letter marks the most explicit public statement to date from the US administration on the possible consequences of automatic budget cuts on the intelligence services.

Until now, senior officials have focused their comments on the impact of budget reductions on the US military and numerous domestic government programs.