The Jordanian authorities, fearful of a wave of immigration from among the 34,000 Palestinian refugees estimated to be living in Iraq, closed the border after a group of Palestinians arrived on Sunday.
The refugees have been placed in a camp in no man's land between Jordan and Iraq, after the Iraqi authorities refused to allow them to return.
Jordanian authorities closed the border to "prevent whoever does not have valid travel documents from entering the country," said Major Bashir al-Da'ajah, a spokesman for the Public Security Department
Nasir Joda, a Jordanian government spokesman, said the Palestinians were denied entry because because they did not have the correct entry permits, Aljazeera reported.
An official from the UN refugee agency said it had sent staff to the desolate border area to assess the Palestinians' plight.
"We are assessing on the ground the situation of 89 Palestinians including 42 children who are now stranded...they are fleeing persecution in Iraq," UNHCR spokeswoman Yara Sharif said.
The UN body says about 23,000 Palestinians are registered as refugees in Baghdad, many of whom fled their homes after the creation of Israel in 1948.
Palestinians fear being swept up in security offensives in Iraq against insurgents behind suicide bombings that have killed thousands of people.