A spokesperson at Aras an Uachtarain told the Sunday Independent it was "inappropriate" to question the President on his spiritual views.
The response comes after a week of disquiet and public dismay that the president omitted any mention of Christ in his televised public address to a nation that remains overwhelmingly Christian.
This is the third year Mr Higgins chose to make no mention of 'Christ' or 'Christianity' in his annual address to the nation.
Taoiseach Enda Kenny also made no mention of religion in his Christmas address.
Meanwhile, Defence Forces chief-of-staff Lieut Gen Conor O'Boyle has conveyed his regret for any embarrassment caused to Mr Higgins as a result of a homily given by the Army's head chaplain on Christmas Eve.
Msgr Eoin Thynne, who is head chaplain to the Defence Forces, used his homily at Windy Arbour Church, Dublin, to comment on the absence of any reference to the Christian faith in the President's message.
Since that homily, Msgr Thynne has also voiced concerns about the crib allegedly being removed from the Defence Forces headquarters in Newbridge, Co Kildare. He said these concerns had been raised with him by others.
Lieut Gen O'Boyle contacted Aras an Uachtarain to "convey the regret of the head chaplain for any embarrassment that may have been caused to the President".
A forces spokesman declined to comment on the claim the crib was removed from the Newbridge headquarters or on who might have ordered its removal. He also declined to say whether or not Msgr Thynne will be subject to disciplinary action.
Irish leaders have bucked the trend in the Western world in their decision to shy away from any mention of Christ in their Christmas addresses.
Around the world, global leaders made various references to Christ and the Bible in televised speeches watched by millions of people from all denominations.
In Britain, Prime Minister David Cameron who once said that his Anglican faith "sort of comes and goes", turned to the Gospel to illuminate his central theme of 'big society'.
In his
Christmas message, Mr Cameron said that millions of people building the
big society are living up to the teachings of Christ.
He also quoted the 'Act of the Apostles' from the New Testament.
US President Barack Obama,
who came under much scrutiny for his religious beliefs in the run-up to
his election, reflected upon the meaning of Christmas, while still
keeping its significance inclusive of all religions.
Sitting beside the First Lady, Michelle Obama,
he said: "This is our chance to celebrate the birth of Christ and to
live as he taught us to love our neighbours as ourselves, to feed the
hungry and look after the sick, to be our brother's keeper and our
sister's keeper. For all of us as Americans, regardless of our faith,
those are values that can drive us to be better parents and better
friends, better neighbours and better citizens."
Queen Elizabeth
also made reference to Christ in her Christmas message: "For
Christians, as with all people of faith, reflection, meditation and
prayers help us to renew ourselves in God's love as we strive daily to
become better people."
She also drew on the nativity
story, saying: "On the first Christmas in the fields above Bethlehem, as
they sat in the colds of night watching their resting sheep, the local
shepherds must have had no shortage of time for reflection. Suddenly all
this was to change. The humble shepherds were the first to hear and
ponder the wondrous news of the birth of Christ, the first Noel -- the
joy of which we celebrate today."
In Germany, Chancellor Angela Merkel
wished the public "God's blessings".
While, in Rome, Pope Francis made an effort to include non-believers in his message as he reached out to atheists and people of other non-Christian faiths in marked contrast to his predecessor.
While, in Rome, Pope Francis made an effort to include non-believers in his message as he reached out to atheists and people of other non-Christian faiths in marked contrast to his predecessor.
"I invite even non-believers to desire peace," he said in the annual address at St Peter's Square.
A
spokesperson for Aras an Uachtarain said the Irish President had
nothing to add to his Christmas and New Year message, which was issued
on December 22.
However, he referred to a passage in his Christmas address that referenced the spiritual dimension.
"The
message of Christmas, shared by many faiths, invites us to care for one
another and to be, in an ethical sense, one another's keepers," it
said.
His decision not to include Christ has been met with dismay from many quarters.
David
Quinn, of the IONA institute, told the Sunday Independent: "All over
the Western world political leaders are not so hidebound by political
correctness that they feel they must leave out any direct reference to
the religious aspect or Christian aspect of Christmas but our leaders,
whether the Taoiseach or the President, sanitise their speeches for fear
of causing offence to the very easily offended. Because who in fact
would be offended by a direct reference to Christianity in a Christmas
message except a dyed-in-the-wool crank?"