Alex Salmond yesterday joined the fierce war of words between Westminster and Holyrood ministers over the use of stop-and-search powers by British Transport Police.

The First Minister backed his Justice Secretary, Kenny MacAskill, who came under criticism from the UK transport minister who has responsibility for the force that polices the rail network in Britain.

Last weekend, Mr MacAskill complained that the British Transport Police (BTP) threaten community relations with extensive use of the stop and search powers since the terror attack on Glasgow Airport in June, saying they were following a "diktat from London".

Nearly 15,000 checks have been carried out at rail stations, while the eight Scottish-based forces have chosen to use the powers fewer than 150 times in nearly a year. Of the BTP checks, the police believe 12% were on people from ethnic minorities, compared with a 2% share of the population.

That provoked the strongest attack on the SNP government from a Whitehall minister. Tom Harris, who is Labour MP for Glasgow South, said the Scottish Justice Secretary had been "cynical and irresponsible".

In a letter to Mr MacAskill, he said it was "unacceptable" to base his comments on hearsay without discussing it with the BTP.

"Kenny MacAskill is playing politics with anti-terrorism operations," Mr Harris said.

The SNP came under attack from Conservatives and LibDems for making a political controversy out of policing. David McLetchie, the former Scottish Tory leader, said the SNP should give "full support to all police forces rather than sitting, carping and undermining them from the sidelines".

Mr Salmond told MSPs: "It is entirely appropriate that the Cabinet Secretary should question these matters in terms of the public interest." He turned on Mr Harris for responding through a press release: "It is inappropriate to conduct debates in that fashion."

Today, Mr Harris is scheduled to be in Glasgow on patrol with the BTP.