Only 395 Town fans will be allowed into the Interlink Express Stadium for the first round clash a week on Sunday, which is being screened live by the BBC, starting at 1pm.
Town officials made efforts yesterday to get the FA-stipulated 15% of capacity - around 650 seats - but they were rejected.
Club secretary Ann Hough said: "The Accrington club were happy to let us have more seats, but the safety team weren't, because of intelligence relating to our matches.
"They believe Huddersfield Town fans will cause problems - as was the case at Lincoln - so they want as few there as possible."
The news comes just two weeks after Town pledged to ban for life anyone convicted of a football-related offence at matches home or away.
Town's safety officer, Sue Watson, and a team of stewards will be on duty when Town visit Scunthorpe tomorrow, in a further effort to identify troublemakers.
Segregation at Conference club Accrington would have allowed them a section for 1,700 or 1,300 Town fans. But most of that will now be a home area and a sell-out is on the cards.
Town's tickets are £10 (adults) and £6 (concessions). They will go on sale to season-ticket holders only from 9am tomorrow on a strictly one ticket for one voucher basis.
No advance bookings will be accepted, although tele phone bookings will be accepted from 9am while tickets last.
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