Indonesia's central bank governor Perry Warjiyo resigned on Monday for personal reasons, prompting President Prabowo Subianto to appoint senior deputy governor Destry Damayanti as interim chief in a surprise move that unsettled financial markets and renewed concerns about the independence of Bank Indonesia.

Warjiyo submitted his resignation on Saturday, with State Secretariat Minister Prasetyo Hadi confirming President Prabowo had accepted it before markets opened in Jakarta. Prasetyo said the president had not yet nominated a permanent successor, while urging investors to remain calm and promising a transparent appointment process that would not disrupt monetary policy or economic stability.

Destry, who joined Bank Indonesia's board after serving as chief economist at Bank Mandiri and as a commissioner at the Indonesia Deposit Insurance Corporation, sought to reassure markets that policy continuity would be maintained. "BI will always ensure the continuity of its duties and authorities" to maintain the stability of the rupiah and the financial system, she said, adding that the central bank would continue to operate in line with best practices.

The announcement weighed on financial markets, with the rupiah weakening by as much as 0.36 per cent against the US dollar and Jakarta's benchmark stock index swinging between gains and losses. Reuters reported that analysts linked the reaction to uncertainty over the future leadership of the central bank and concerns that its independence could come under greater political pressure.

Bhima Yudhistira Adhinegara, executive director of the Center of Economic and Law Studies, told Reuters that "what must now be anticipated after Perry's resignation is the weakening of Bank Indonesia's independence", warning that rebuilding investor confidence would be difficult if political pressure continued.

Angus Mackintosh, an ASEAN specialist at Aletheia Capital in Singapore, told CNBC that markets would closely scrutinise the choice of a permanent governor, adding that any appointment perceived as politically connected could raise further concerns because "BI should remain independent".

Warjiyo's departure follows months of debate over the central bank's role in supporting President Prabowo's economic agenda. Parliament last month approved legislation strengthening Bank Indonesia's responsibility to support growth while giving lawmakers greater influence over the central bank and financial regulators.

Rating agencies Moody's and Fitch cited concerns over those changes when revising Indonesia's credit outlook to negative earlier this year, although S&P maintained a stable outlook, saying it did not expect the revised mandate to fundamentally erode the bank's operational independence.

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