'No Amnesty International India employee shouted any slogans at any point,' the organisation said in a statement
Amnesty denied that its staff made anti-nationalist comments at one of its events on disputed Indian Kashmir after the rights group was slapped with sedition charges on Tuesday.
Police in the southern Indian city of Bangalore filed the initial charges against Amnesty on Monday following complaints that event participants called for independence of the volatile Kashmir region.
Sedition charges, which carry a maximum penalty of life in prison, have been used previously against supporters of independence for Kashmir, which is divided between India and Pakistan but claimed in full by both.
The case comes at a particularly sensitive time, with large parts of Indian Kashmir under curfew following weeks of deadly violence between protesters and security forces.
Security forces shot dead five people and wounded another 20 during fresh protests in the Himalayan region on Tuesday, according to witnesses and security sources.
"No Amnesty International India employee shouted any slogans at any point," Amnesty International India said in a statement on Saturday's event in Bangalore.
"The focus of the event was squarely on allegations of human rights violations and the denial of justice in Jammu and Kashmir."
Rights campaigners have long accused New Delhi of using the British-era sedition law to clamp down on dissent, although convictions are rare.
The charges come as foreign charities are under intense pressure in India, with the government saying last year it has cancelled the overseas funding licences of around 9,000 non-governmental organisations in a major crackdown.
The complaints were lodged with police by a Hindu nationalist student organisation, some 200 of whose members staged protests outside Amnesty's offices in Bangalore.
"We want the organisers and those who raised anti-India slogans to be arrested and jailed," student organiser Prem, who uses one name, told reporters, as police dragged scores into buses and vans to break up the rally.
Bangalore police said they were probing the complaint and studying footage of the event at the city's United Theological College to identify those who shouted "anti-India" slogans.
"We have booked a case of sedition and rioting under various sections of the Indian penal code against Amnesty on a complaint that anti-India slogans were raised at an event it organised," deputy police commissioner T.R. Suresh told AFP.
In an earlier statement, Amnesty said police had been invited to monitor Saturday's event, at which Kashmiri families spoke of alleged abuses of relatives by security forces.
"The filing of a complaint against us now, and the registration of a case of sedition, shows a lack of belief in fundamental rights and freedoms in India," Amnesty International India chief Aakar Patel said.
Indian forces have since 1989 been fighting militant groups seeking either independence for Kashmir or a merger with Pakistan. Tens of thousands of mainly civilians have been killed in the fighting.