The move against the journalists was widely condemned
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A move to deploy federal security forces outside a newspaper office in south India has been criticised.
The chief minister of Tamil Nadu state has written to the federal government strongly objecting to the decision.
Security has been stepped up at the offices of the English daily The Hindu in the state capital, Madras.
It followed a request from the newspaper's chief editor who said his staff was being harassed and intimidated by the state police.
In a letter to Indian Home Minister, LK Advani, Chief Minister Jayalalitha described the move as "unwarranted and against the spirit of federalism".
She said there was absolutely no threat to the editor or the staff of the paper and the move would cause irreparable damage to the state government's relations with Delhi.
Relations worsened between Ms Jayalalitha and The Hindu last week after the state assembly ordered the arrest of six journalists, five of whom work for the daily.
But on Monday, India's Supreme Court halted the order.
The journalists had been sentenced to 15 days in jail for writing articles critical of Ms Jayalalitha.
Journalists and politicians described the state assembly's move as an attack on democracy.
'Gross abuse'
Journalists across India have rallied round the 125-year-old newspaper, with protests in the Tamil Nadu capital, Madras, as well as in the national capital, Delhi.
The leader of the opposition Congress Party, Sonia Gandhi, said: "Such high-handed action by the state legislature is a threat to our democracy."
The committee of the Tamil Nadu state assembly objected to some descriptions of the chief minister contained in the paper last April, and invoked the right of legislative privilege to sentence the six to prison.
The Hindu has maintained the articles were simply "a rather measured criticism of the chief minister".
The journalists, including one from a Tamil newspaper, have evaded arrest and their whereabouts are now a secret.
This case is a sign of the ever-worsening relations between Ms Jayalalitha, a former film star and one of India's most controversial politicians, and one of India's most respected dailies.
Media associations in Delhi said the prison sentences were "a gross abuse of legislative authority".
Senior journalists in Delhi have said it goes further and amounts to an attack on the entire press.