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The policy is arbitrary, hard to understand and is unacceptable to the Indonesian Government
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Indonesian foreign ministry spokesman
The measures were introduced in the wake of the 11 September terrorist attacks but have drawn widespread criticism from the 25 countries affected.
Pakistan's Foreign Minister Khurshid Mahmud Kasuri, who is leaving on his first visit to the US on Saturday, called for the measures to be suspended.
"Pakistan has been at the forefront of the war against terrorism... It's unfair to bracket us with other countries," he said.
Washington put Indonesia, along with Egypt, Jordan, Kuwait and Bangladesh, on its list of countries affected on Thursday.
The Indonesian government has responded by urging its citizens to postpone non-essential travel to the US while it "studied" the US move.
An Indonesian foreign ministry spokesman criticised the measures as "arbitrary, hard to understand and unacceptable".
Indonesia's Foreign Minister Hassan Wirayuda was expected to raise the issue with the top US envoy to Asia, James Kelly, who arrived in Indonesia on Friday as part of a regional tour.
Mr Kelly also met with Indonesian President Megawati.
'Discriminatory'
The new measures will affect thousands of Indonesian men who visit the US as students, tourists or to do business.
The US says the new rules are needed to track terrorists who enter the US.
Males over the age of 16 from affected countries must register with the US Immigration and Naturalisation Service, where they have their photos and fingerprints taken and documents examined.
But critics say that countries are being added to the list because they are Muslim, not because they present a terrorist threat.
Of the 25 countries listed so far, only North Korea is not predominantly Muslim.
Long term visitors from the listed countries who are already in the US must register with immigration authorities between 24 February and 28 March.