The museum said the map was an "oversight" that had been rectified.
The map, one of several aiming at placing exhibits in their geographical context, was located in the children's section of the museum.
The error was pointed out on January 19 by Qatar Museums Chairperson HE Sheikha al-Mayassa bint Hamad bin Khalifa al-Thani, who retweeted a picture of the map showing Bahrain and the Gulf coast with blank sea in the place of Qatar.
"Throughout history museums were a source of reference. People would visit to acquire knowledge and learn about world cultures through the exploration of objects on display. Although the notion of museums is a new one to Abu Dhabi, surely the @MuseeLouvre is not okay with this?" she wrote.
The following day, Anwar Gargash, Emirati minister of state for foreign affairs, said it was "a slight oversight" that Qatar blew out of proportion.
Analysts said it was mischievous on the part of the Emirati minister to play down such a grave mistake and blame Qatar for blowing it out of proportion. "It requires much impudence to display a map in a museum that omits a neighbourly country and then justify it as a slight oversight," he said, adding "culture" would have meant owning up the mistake and issue an apology.
Last week, Washington Institute's Simon Henderson also reported that a map at the museum had "completely" omitted Qatar.
"In the children's section of Abu Dhabi's new flagship Louvre Museum, a map of the southern Gulf completely omits the Qatari peninsula - a geographical deletion that is probably incompatible with France's agreement to let Abu Dhabi use the Louvre's name," Henderson wrote.
Many twitter users, both local and international, had expressed ire on the Louvre omission while several others made fun of the museum for the "brazen and deliberate" measure.
The Louvre Abu Dhabi was inaugurated with great pomp in November by French President Emmanuel Macron and Abu Dhabi's Crown Prince Mohamed bin Zayed al-Nahyan.
It was marketed as "a universal museum" celebrating cultural exchange and tolerance.
The UAE-Qatar relations worsened last year when Saudi Arabia, the UAE, Bahrain and Egypt in June cut all ties with Doha, including land, sea and air links.
They accused Qatar of ties to Islamist extremists and being too close to Iran.
Doha rejects the accusations and maintains that the blockading states are seeking to take over its foreign policy.
Following the Qatar "omission", a new map published by the Louvre Abu Dhabi Museum appears to have removed the border demarcation between UAE and the Omani territory of Musandam, Al Jazeera has reported.
According to images published on social media, the new map shows Musandam, an exclave of Oman in the northern tip of the peninsula, as part of the UAE, the Doha-based pan-Arabic TV channel said.
On social media, some Omani activists accused the museum of deliberately trying to distort the geography of the Gulf.
"The Louvre Abu Dhabi is lying and deliberately spreading misinformation," said Twitter user @BARQ_OMAN1.
Twitter user @MajedFakhar said it was second time the UAE had "annexed" Musandam in recent months after a map published on the Mohamed bin Zayed Award for Best GCC Teacher also removed the demarcation line.