The announcement on June 18 by Georgia's State Agency for National Heritage Preservation could have major political repercussions for President Mikheil Saakashvili, who had strongly backed the reconstruction project.
The 11th-century cathedral, which is currently cloaked in scaffolding, is widely regarded as a masterpiece of medieval Georgian architecture.
It has been listed as a World Heritage site by the United Nations' scientific and cultural organization UNESCO.
For some time, however, UNESCO officials have been voicing concern about the planned restoration of the cathedral in Georgia's second city, Kutaisi, saying the work risks distorting the structure's original look.
A report the organization published in 2011 warned that the interventions that had been carried out at the cathedral thus far were "almost irreversible."
RFE/RL's Georgian Service reported last week that UNESCO had even warned that the monument is in very real danger of being removed from its list of World Heritage sites if the restoration continues.
Halting work on the cathedral is likely to be a major disappointment to Saakashvili, who had called for the restoration to be completed by October.
If that deadline had been met, it would presumably have given the president a timely boost ahead of parliamentary elections that are scheduled in the same month.
Named after Bagrat III, the first king of a unified Georgia, the ancient cathedral is seen as a symbol of the unity of the Georgian state, an idea that still resonates strongly in the Caucasus country, which has two breakaway provinces under the control of separatist rebels.
By restoring Bagrati Cathedral, it's possible that Saakashvili had hoped to strike a chord with many Georgians who also wish to see the country's traditional borders restored as well.
Provided work eventually resumes on the cathedral, the Georgian leader will now have to wait for presidential elections next year to try and reap the political capital that is to be gained from renovating one of the country's most potent symbols.
Then again, if UNESCO decides to definitively remove the cathedral from its World Heritage List at a meeting in St. Petersburg on June 24, Saakashvili's strong backing for the Bagrati restoration project could have political ramifications that are the opposite to what he intended.
Written by Coilin O'Connor with contributions from RFE/RL correspondent Merkhat Sharipzhanov and RFE/RL's Georgian Service
PHOTO GALLERY: Georgia's Bagrati Cathedral