The change of guard in the administration of the 12th century shrine comes in the midst of a state-wide outcry over the missing keys of the inner chamber of the Ratna Bhandar of the Jagannath Temple in Puri.
Mr Mohapatra, an IAS officer who is principal secretary in the school and mass education department, has been given additional charge of chief administrator SJTA, an official in the Chief Minister's office said.
Mr Jena, also an IAS officer, had been the chief administrator of the SJTA for over two years.
Mr Mohapatra has been entrusted with the additional responsibility ahead of the annual Rath Yatra of lord Jagannath scheduled to be held on July 14.
Earlier in the day, Mr Jena held a meeting of the servitors in connection with the Supreme Court's ruling to prevent exploitation of devotees by staff at the temple.
In its order, the apex court asked the Puri district judge to file an interim report by June 30 on the factual aspects such as difficulties faced by the devotees, exploitative practices and deficiencies in the management, if any.
Puri district judge Ambuj Mohan Das, Collector Aravind Agarwal and SP Sarthak Sadangi also attended the meeting.
"Though the servitors knew about the SC direction, today we in presence of the district judge officially informed them details of the order," Mr Jena said.
"We have also requested the servitors to abide by the Supreme Court's directives and asked them to cooperate with the administration," he said.