A man accused of carrying out the single worst atrocity of the Troubles in Northern Ireland, the killing of 29 people in the 1998 Omagh bombing, has been remanded in custody.

Seamus Daly, 43, a prominent supporter of the Irish republican cause, was denied bail by a judge at Dungannon Magistrates’ Court as police kept guard outside.

No-one has ever been convicted in a criminal court over the bombing, which tore through the market town only months after the signing of peace accords which largely ended three decades of sectarian violence in Northern Ireland.

However, relatives of some of the victims brought a civil action against five men they claimed were responsible, including Daly.

In 2009, the Belfast High Court found that Daly and three other men were liable and they were later ordered to pay more than STG1.6 million ($A2.9 million) in damages to the relatives – money they are still pursuing.

Daly has always denied involvement in the bombing.

Unshaven and dressed in jeans and a dark grey hooded top in the half-hour hearing on Friday, he was refused bail on the grounds that he might try to flee across the border to the Republic of Ireland.

A detective told the court Daly was arrested as he accompanied his heavily-pregnant wife to a hospital maternity unit on Monday.

Daly claimed to be his brother when stopped by police but was identified through fingerprint analysis.

He has been charged with 29 counts of murder, two additional offences linked to the Omagh explosion and two linked to an attempted explosion in Lisburn in April 1998.

The prosecution case is based on phone, forensic and witness evidence, the unidentified detective told the court.

Daly’s lawyer Dermot Fee said there were “significant weaknesses” in the case.

Daly was remanded in custody until May.