The cellars, remaining closed for several decades, were ordered to be opened by the apex court to prepare an inventory while considering a private petition recently.
The examination was conducted but the media was kept away as its result was meant to be informed only to the Supreme Court.
The apex court had appointed Justices M N Krishnan and C S Rajan as observers.
Additional Chief Secretary K Jayakumar, temple executive officer Harikumar, petitioner T P Sundararajan and a representative from Archaeology Department and two representatives of Travancore King Marthandavarma were also present while the chambers were opened.
"We will open four of the six chambers today and prepare a detailed inventory of all assets within it. We will convene a meeting on Friday to discuss details of the process. The date of the opening of the other two chambers will be decided then," Justice Krishnan said just before opening the chambers.
"To examine the stability of the centuries-old chambers, we are planning to include a chief engineer also in Friday's meetings, he said.
A detailed report of the assets will be prepared and submitted to the Supreme Court soon and they would not be shared to media or others before that, Justice Krishnan said.
The entry of media and common people was strictly restricted inside the temple when the chambers were opened.
Police were also deployed in the premises of the centuries-old shrine to ensure the smooth process.
The magnificent temple is known for its architectural elegance and long rows of granite columns with exquisite engravings have Lord Vishnu reclining on the thousand-headed serpent Anantha as the presiding deity.
The temple is run by a trust floated by the Travanacore royal house, to which Lord Padmanabha is the family deity.
The court issued orders on a private petition which sought measures for greater transparency and accountability in the management of the temple.