Amnesty International secretary general Irene Khan said the treatment of the minority Ahmadiya sect in her native Bangladesh was "very worrying."
Bangladesh earlier this month banned publications by the sect following pressure from Islamic hardliners allied with Prime Minister Khaleda Zia's government to declare the sect non-Muslim.
Khan, in Bombay for the World Social Forum, noted that the government had at the same time effectively ensured the security of an Ahmadiya mosque that was under threat.
"It is a very worrying sign that the government is sending mixed messages," Khan told AFP on Sunday.
"In situations like this, you have to nip in the bud the start of the trend towards intolerance," she said.
The Ahmadiya movement was founded in the late 19th century in what is now Pakistan with the professed goal of reviving Islam by stressing non-violence and tolerance.
The sect breaks sharply with mainstream Islam by not insisting Mohammed was necessarily the last prophet.
Khan said there were "two Bangladeshes": one that has witnessed "a growth in abuse without accountability," including attacks on the Hindu minority, and another with dedicated groups committed to women's rights, children's rights and other issues.
She said the problems in Bangladesh, which is deeply polarised between its two major parties, did not originate with the election of Zia in 2001.
"Bangladesh has for some time now seen a failure of governance," she said.
More than 100,000 people are taking part in the World Social Forum, a yearly meet of anti-globalisation activists