The sets, previously damaged about 40%, dated back to about 250-300 years ago.
They measure 22m and 18m in length, with the first being believed to be among the largest in Vietnam so far.
The mammals are both nearly 4m high and have 50 vertebrae on their spine, along with 28 pairs of ribs. The skulls are 4m wide.
A project to restore the skeletons and build an exhibition area for conservation, cultural studies and tourism development was carried out with a budget of VND14 billion (US$616,470).
Ly Son island currently has seven whale temples which are home to dozens of skeleton each.
The temples, known as Lang Ong, are often seen in coastal fishing villages in Vietnam, reflecting an old fishermen’s belief in the whale’s power to guard their lives at sea.
Fishermen also express respect for the giant ocean mammals when they find them dead, and perform a respectful funeral.