The American Consulate in New York has compiled a list of 20 Irish people it is particularly concerned about.
An additional 70-plus missing people remain on the Department of Foreign Affairs' database.
A Department spokesman said he expected most of them could be eliminated from the list in the next few days.
He did warn, however, that there might be more Irish citizens who have not been reported missing. Among those who have not been heard from since Tuesday are Ms Joanne Cregan from Churchtown, Dublin.
Ms Cregan, who is in her 30s, worked on the 105th floor of the north tower, the first building to be hit in the terrorist plane attack.
A spokesman for the Cregan family last night said her relatives were "distraught" and "hoping against hope" that she had not been harmed.
She had been employed by Cantor Fitzgerald, the financial securities company, for a number of years.
Mr Seβn Canavan (39), a New York carpenter with Irish parents, was also working in the World Trade Centre on Tuesday last.
He is understood to have called his sister after the first plane hit but has made no contact since.
Mr Canavan is a cousin of Co Tyrone GAA footballers Peter and Pascal Canavan. His father, from Tyrone, and mother, from Armagh, emigrated from Ireland in the 1950s to Long Island, New York, where Mr Canavan was born.
Members of his immediate family still resident in Ire land are travelling to New York this week.
Also missing is Mr Damien Meehan (33), a financial adviser whose family come from Donegal town.
He was in the 88th floor of the north tower when it was hit by the first plane, and made a phonecall to his brother, a firefighter with the New York Fire Department, telling him the building was filling with smoke and asking how could he get out.
Mr Meehan's wife, Joanne, is expecting their second child.
His parents have been living in Manhattan since the 1950s.
Speaking from Donegal, his uncle Mr Hugh Meehan said his family "were going over and back to the hospitals and the site and have heard nothing yet.
It's a very difficult time for him".
Missing too is Mr Eamon McEneaney (46), a financial consultant, who was employed on the 104th floor of the south tower.
A father of four, Mr McEneaney came with his family to their Irish homestead at Castleblayney, Co Monaghan each summer and this year he planned to return for a family reunion in Dublin next weekend.
His cousin-in-law, teacher Ms Maureen McEneaney said yesterday : "We are all numbed by the tragedy - he was a real gentleman with a heart of gold and loved visiting the area."
Other missing Irish citizens include Ms Ann McHugh (35) from Tuam, Co Galway; Mr Martin Coughlan (53) from Cappawhite, Co Tipperary, and Mr Kieran Gorman (35) from Carrowcurragh, Lavagh, Co Sligo.
Meanwhile, the number of Irish people confirmed dead by the Department of Foreign Affairs remains at four.
Ms Ruth Clifford McCourt (44) and her four-year-old daughter Juliana, from Cork, and Mr Patrick Currivan (53) from Dublin, were on the hi jacked United Airlines plane that crashed into the south tower.
The chaplain of the New York Fire Department, Father Michael Judge (68), whose parents came from Co Leitrim, was giving the Last Rites to a crew member when he was was killed by falling debris from the collapsing towers.
The final death toll of Irish victims is expected to reach double figures, according to the Department of Foreign Affairs.
Meanwhile, two Americans missing after the World Trade Centre attacks will be prayed for at a special Mass in Roscommon in the church where they recently attended a friend's wedding.
The pair, Mr Chris Jones and Mr Aaron Horowitz, were guests at the wedding of Ms Eileen Connaughton, a New York accountant, and Mr James Montague, a bond trader from London, three weeks ago at the Sacred Heart Church in Roscommon Town.
Ms Connaughton is the daughter of Mr Terry Connaughton, formerly of Athleague, Co Roscommon, who moved to America in the 1950s.
Mr Connaughton, former president of the New York GAA, returned to Ireland yesterday and began to put arrangements in place for the service.
"The Mass is being organised specifically for prayers for the missing men and all the other injured and deceased and their families," Mr Connaughton said.
At the weekend, five Department of Foreign Affairs officials joined Irish consulate staff in New York.
They will assist relatives of missing Irish people who travel to America over the next few days, following the resumption of transatlantic flights.
"They are going over to strengthen the consulate, which has 15 people working on a 24- hour basis," a spokesman said.
The Department has again urged families to notify staff as soon as they hear their loved ones are safe.
The freephone numbers are: 1 - 800 715 165; 1 - 800 715 159; 1 - 800 401 800; and 1 - 800 385 858.