Following revelations in the Italian media, the Anglo-Dutch group said that its offices had been "visited" by anti-fraud investigators.
"We can confirm that representatives of the Dutch Financial Intelligence and Investigation Service (FIOD) and the Dutch Public Prosecutor recently visited Shell at its headquarters in The Hague," a spokesman said.
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"The visit was related to OPL 245, an offshore block in Nigeria that was the subject of a series of long-standing disputes with the Federal Government of Nigeria. Shell is cooperating with the authorities and is looking into the allegations, which it takes seriously."
Italian daily Corriere della Sera reported earlier that the Dutch investigators were working in collaboration with Italian prosecutors looking into Shell and Italian energy group ENI's 2011 acquisition of joint exploitation rights to OPL245, which is estimated to contain up to nine billion barrels of crude.
Prosecutors in Milan have been investigating ENI executives involved in the deal since 2014.
Under the licensing accord, ENI made a payment to the Nigerian government of $1.09 billion to secure joint ownership while Shell, which already owned a 40-per cent stake, handed over $200 million.
Most of this money was subsequently passed on to Malabu Oil and Gas, a company believed to be controlled by Chief Dan Etete, a former Nigerian Oil Minister.
In an episode that has come to be regarded as emblematic of Nigeria's problems with corruption, Etete had awarded the rights to the block to Malabu in 1998, at a time when he was close to Nigeria's then-military dictator General Sani Abacha.
The probe into ENI was triggered after an intermediary in the deal, Emeka Obi, sued Malabu in Britain's High Court and won an order that the company pay him $110 million in unpaid fees.
ENI has always maintained that its actions in Nigeria have been beyond reproach and that all the money it had paid in Nigeria had gone directly to the government.
Shell also insisted it had not been involved in any wrongdoing. "Shell attaches the greatest importance to business integrity," a spokesman said.
"It's one of our core values and is a central tenet of the principles that govern the way we do business. All employees are expected to uphold these principles and failure to do so will result in consequences up to and including dismissal.