A bench of justices R M Lodha and A K Patnaik said the amount for strengthening the vaults, which is estimated to cost Rs 80 lakh, would be paid jointly by the state government and the temple management.
It said the two third of the cost would be paid by the state and the rest would be paid by the management.
The apex court-appointed expert committee, meanwhile, said that the whole process of unearthing the assets and its valuation would be completed by June 1 next year.
The temple has six vaults, most of which are underground and are filled with priceless articles. During preparation of its inventory recently by the apex court-appointed panel, five of these vaults were opened, leaving out one chamber, called 'vault B'.
The apex court had appointed expert committee for scientifically documenting the priceless temple's treasure. The panel comprises experts from ISRO, the Centre for Development of Advanced Computing (C-DAC), the Centre for Earth Sciences Studies and top officials of the Kerala police.
The sprawling temple, an architectural splendour in granite, was rebuilt in its present form in the 18th century by the Travancore Royal House, which ruled southern Kerala and some adjoining parts of Tamil Nadu before integration of the princely state with Indian Union in 1947.
Even after independence, the temple continued to be governed by a trust controlled by the erstwhile royal family, to whom Lord Padmanabha (Vishnu in reclining posture) is their family deity.