The refugees were among those driven from their homes around Mosul last summer in an offensive by the jihadist Islamic State group (IS), and the pontiff used a satellite phone connection provided by Catholic channel TV 2000 to offer them his support.
"Dear brothers, I am close to you, very close to you in my heart," the pope was quoted as telling the refugees by Italian press agency AGI.
"The children and the elderly are in my heart," Francis also told the Iraqi refugees in the Ankawa camp, just hours before celebrating midnight mass in Saint Peter's basilica.
"Innocent children, children who have died, exploited children.... I am thinking, too, about grandparents, about the older people who have lived their lives, and who must now bear this cross."
On Monday, the pope addressed a long letter of support to Christians in the region, urging them to "persevere" despite the difficulties they face.
In it, he denounced IS as a "terrorist organisation of a size that was unimaginable before, committing all types of abuses... (and) striking some among you who have been brutally chased from your lands, where Christians have been present since apostolic times."
Francis lamented the suffering of women, children and the elderly who "must face the harshness of winter without a roof," and called for concrete support from the wealthier churches.
Pope calls for greater empathy in Christmas Eve mass
Pope Francis urged people to have greater empathy towards family and friends with problems in his Christmas Eve mass on Wednesday, saying the world "needs tenderness" and warmth.
"Do we have the courage to welcome with tenderness the difficulties and problems of those who are near to us?" the Argentine asked in his traditional homily given in Saint Peter's Basilica at the Vatican.
"Or do we prefer impersonal solutions, perhaps effective but devoid of the warmth of the Gospel? How much the world needs tenderness today!" he said.
The short address laden with Gospel references was a far cry from his barbed Christmas speech to cardinals, bishops and priests on Monday.
In an unprecedented outburst, the 78-year old lambasted the Vatican's bureaucracy, listing 15 "ailments" within the Church, including lust for power and "spiritual Alzheimer's", which he hoped to see cured in the new year.
Among the ills was lack of empathy, with the pope warning against "the sickness of indifference towards others, when each person thinks only of themselves and loses the sincerity and warmth of human relationships."
In the Christmas Eve address, the leader of the world's 1.1 billion Roman Catholics called on "the arrogant, the proud... (and) those closed off to others" to meet life "with goodness, with meekness."
"The presence of the Lord in the midst of his people cancels the sorrow of defeat and the misery of slavery, and ushers in joy and happiness," he said.
The mass was broadcast live in 3D for the first time, with images of the crowds of faithful massing in and around the tiny city state captured by drones.
The festivities continue Thursday, Christmas Day, with the pope delivering his traditional "urbi et orbi" message "to the city and the world" at 1100 GMT.
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