The European Commission is struggling to contain the damage from a bribery scandal that precipitated the resignation of John Dalli as European commissioner for health and consumer policy.

As Dalli hit back against the allegations, accusing José Manuel Barroso, the Commission president, of forcing the resignation, the Commission was last night fending off claims that its planned tobacco legislation had been ambushed.

Dalli, a former finance and foreign minister of Malta, categorically denies the case made by OLAF, the European Union’s anti-fraud office, that he was aware that an entrepreneur from Malta was trying to extract money from a Swedish tobacco company in return for persuading Dalli to change his tobacco proposals.

OLAF submitted its report to the Commission on Monday (15 October) and Dalli’s resignation was announced the next afternoon. Dalli later said that Barroso had threatened to sack him and that he not been given the opportunity to respond to the allegations against him. The Commission said that Dalli chose to resign to defend his and the Commission’s reputation. He became the first European commissioner ever to resign for reasons of impropriety.

Malta must now nominate a replacement to send to Brussels, who will have to win the approval of the European Parliament and the Council of Ministers. Amid signs that this could be a difficult process, the future of Dalli’s policy portfolios in the Commission is unclear.

Barroso announced on Tuesday that Maroš Šefcovic, the commissioner for inter-institutional relations and administration, would take temporary charge of Dalli’s dossiers. But yesterday the Commission said that Šefcovic would not be replacing Dalli on a planned trip to India next week (25-28 October).

A Commission spokesman also said that the new Maltese commissioner might not be given responsibility for the same dossiers that Dalli had had – raising the possibility of a re-shuffle. It would be the first change to the line-up of commissioners since the Barroso II Commission took office in February 2010.

The Commission said yesterday that Dalli’s resignation would not affect work carried out on draft legislation in the areas of health, food and consumer policy. Dalli was planning to announce stricter rules on cigarette packaging before the end of the year and there is now some doubt about whether this will happen.

The report by OLAF will now be sent to the public prosecutor in Malta who will decide on whether to take action.

The scandal has put the behaviour of lobbyists in the spotlight. The tobacco industry has been involved in intense lobbying to try to stop Dalli from proposing tough rules on cigarette packaging. The allegation against Dalli was brought by Swedish Match, a manufacturer of the smokeless tobacco product snus, raising suspicions among anti-tobacco campaigners that Dalli had fallen into a trap.

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Giovanni Kessler, the director-general of OLAF, said yesterday that his office had investigated the possibility that Dalli had been set up but concluded that this was not the case.

Nevertheless, cigarette companies used the opportunity of his resignation to call for the proposal on tobacco products to be delayed.

A statement released by the Commission said that the OLAF investigation “found that the Maltese entrepreneur had approached the company using his contacts with Mr Dalli and sought to gain financial advantages in exchange for influence over a possible future legislative proposal on snus”.

It added: “No transaction was concluded between the company and the entrepreneur and no payment was made.”

“The OLAF report did not find any conclusive evidence of the direct participation of Mr Dalli but did consider that he was aware of these events.”