An expert on Indonesian militant groups has criticised a decision to expel her from the country.
Sidney Jones criticised Indonesia's intelligence authorities
Sidney Jones, an American analyst from the International Crisis Group (ICG), said she was issued with the expulsion order on Tuesday.
Immigration officials said she was asked to leave due to visa violations.
But Ms Jones said the expulsion order may have been prompted by her recent criticism of Indonesia's army and intelligence agencies.
"I was devastated to learn that I had to leave Indonesia, but now I am just furious," Sidney Jones told the Associated Press news agency on Wednesday.
As the director of the ICG in Indonesia, Ms Jones is regarded as an expert on the region's militant groups, in particular Jemaah Islamiah, which has been linked to the Bali bomb attacks in 2002.
She said no official reason had been given for her expulsion, nor had any government figure formally told her what she had done wrong.
But the order comes just days after the head of Indonesia's intelligence services told a parliamentary committee that ICG and 19 other unnamed local non-governmental organisations were a threat to national security.
The ICG's chief, Gareth Evans, said the expulsion order was a blow to press freedom in Indonesia and was driven by "a desire to smother legitimate criticism".
"To shoot the messenger doesn't say much for the state of political liberty in Indonesia under the Megawati government," the Reuters agency quotes him as saying.
President Megawati Sukarnoputri is gearing up for elections on 5 July. Opinion polls show her trailing her main rival, Susilo Bambang Yudhoyono.
Mr Yudhoyono criticised the expulsion order, saying the government had to properly explain what was going on.
Ms Jones' work examined the rise of extremism in Indonesia
"Let us hope the expulsion does not damage the democracy that we are
building," he told reporters on the campaign trial.
Human rights activists fear Ms Jones and her Australian colleague Francesca Lawe-Davies - who has also been issued with an expulsion order - are being punished for speaking out against sensitive government policies.
The ICG has recently published a number of reports on Indonesia's Islamic extremists, and the separatist conflicts that are simmering in the provinces of Aceh and Papua.
The reports criticise the way these situations have been handled, particularly by the army and intelligence services.
According to Tim Johnston, a BBC correspondent in Jakarta, there is a fear that Indonesia's security organs are again moving to intimidate their critics into silence.