Seven members of the Kopassus special forces, along with three members of the regular Indonesian army, are coming to the end of a one-year MA course at Hull University.
The course in Security Studies examines "the theory and practice of strategy and security from the perspective of the defence professional". There are just three other students on the course.
During the 32 years of Mr Suharto's iron rule, Kopassus and the rest of the military have been linked to a number of atrocities in Indonesia. There is no evidence that the students at Hull have been involved in any atrocities.
In particular, the special forces have been responsible for killing and repression in East Timor, the former Portuguese colony invaded by Indonesia in December 1975. In 1991, 271 unarmed protesters were killed by the military at East Timor's Santa Cruz cemetery.
During the past few months of civil unrest in Indonesia - which led to Mr Suharto's resignation earlier this week - members of Kopassus were on stand-by in support of the riot control police.
"Indonesia has had one of the longest-surviving dictatorships in the world and its special forces like Kopassus have played a crucial role in protecting the status quo," said a spokesman for Tapol, the Indonesian Human Rights Campaign.
"A glance at the bloody history and role of Kopassus will show why Hull University should reject these men."
There is growing controversy at Hull University about the presence of the Kopassus men. Last week the local branch of the Association of University Teachers' (AUT) union passed a resolution demanding that the university should not "support the activities of the security forces" of Indonesia.
A student campaign group also claims the presence of anyone linked to Kopassus could stop other Indonesian students from talking freely about what has been happening in their country.
"There is a great deal of strong feeling here. A number of Indonesian students have felt intimidated," said Zoe Young, one of the campaign organisers.
But the authorities at Hull University have been keen to play down any controversy.
Professor Colin Grant, director of the Centre for Security Studies and a former government adviser in the United States, said that the Kopassus men were all good students.
"The politics of their government are not an issue to me. I am not an expert on Indonesia, I know what I read in the papers," he said.
"I don't think what is happening in their country is any of my business and I don't think it is any of yours."
The university appears to have made strenuous efforts to avoid bad publicity over the presence of the students, who pay up to pounds 6,000 each for the course.
Hull University's head of publicity, Jim Dumsday, is facing disciplinary proceedings after he included in the university newsletter a debate on the issue which took place at a staff meeting.
He now faces the awkward situation of trying to answer questions about the controversy as well as his own role in it.
The university's Registrar, David Lock, who informed him that proceedings were pending, has refused to comment.
The human rights group Amnesty International estimates that since 1975 about 200,000 East Timorese - approximately one-third of the population - have died at the hands of the Indonesian regime.
Funding for the course is available from the Economic and Social Research Council.
A spokeswoman for the council said yesterday that two of the 13 students at present taking the course at Hull were in receipt of grants. She said that grants were available for foreign students, but refused to say whether any of the Indonesians had received money.
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