The head of Bolivia’s recently revived state energy company resigned on Monday, the latest in a series of setbacks to President Evo Morales’s plan to nationalise the country’s gas sector, the second largest in Latin America.

Jorge Alvarado bowed to pressure to step down as the head of YPFB, which is charged with managing the nationalisation policy, after Bolivia’s energy regulator accused him of having signed an illegal contract in June to export discounted crude oil to Brazil in return for refined diesel.

Announcing the resignation – the most high-profile during the government’s seven months in power – Mr Morales said that the YPFB chief had committed “no act of corruption nor harm to the state” and said there was a “conspiracy” to frustrate nationalisation being carried out.

Whether or not Mr Morales’s accusation is justified, the future of the nationalisation process is in doubt. In advertisements in the Bolivian press on Monday, Repsol, the second-biggest investor in Bolivia, threatened to take the Morales administration to court if it continued its “judicial persecution” of the company.

The warning came after officials from the attorney-general’s office in Santa Cruz, the heart of Bolivia’s energy sector, raided the offices of Andina, a Repsol subsidiary, on Friday. They detained Andina’s lawyer and seized documents relating to a 2002 price hedging contract with Brazil that the government says was illegal. The company points out that such contracts are standard industry practice and says it notified the authorities at the time.

The Bolivian government was forced to call a “temporary suspension” this month to its plan to take a greater stake in the country’s gas sector, citing lack of funds and expertise. Last week, the country’s Senate passed a motion of censure against Andrés Solíz, the hydrocarbons minister, for botching the nationalisation and for alleged corruption at YPFB.

That censure vote related to allegations last month by Bolivia’s energy watchdog relating to Mr Alvarado’s approval of the crude-for-diesel swap with Brazil. Víctor Hugo Sainz, the superintendent of hydrocarbons, said that not only would the deal have lost the state $38.5m, but that by authorising an intermediary company to export the crude, Mr Alvarado had contravened the nationalisation decree, which states that only YPFB can sell oil and gas.

Mr Morales had resisted opposition calls to sack both Mr Solíz, refusing his offer of resignation following the Senate censure vote, and Mr Alvarado, who as a former engineer was deemed by the administration to possess the technical skills necessary to implement the nationalisation policy.

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