According to local reports, one crack on the south side of the single arch limestone bridge has spread across four stone blocks. Another on the north side has opened to more than 10mm wide and crosses six blocks.
Engineers are now assessing the safety of the bridge.
It is thought that minor earthquakes in the area over recent weeks caused the cracking.
The original 16th century stone bridge was destroyed by Croatian artillery shells in November 1993 during the Bosnian war.
After a historic campaign the 27m long and 21m high single arch bridge was rebuilt in the same local limestone and reopened three years ago.
The arch links the two halves of the city of Mostar and is supported by limestone abutments linked to wing walls along the cliffs above the river Neretva.
The £5M internationally financed project was hailed as the start of a new era for a municipality which is divided between Croats on the west bank and Bosniaks on the east.
The bridge is now part of a Unesco world heritage site.