MEXICO CITY, Sept 19 (Reuters) - Mexican state energy company Pemex has resumed dealing with Vitol, three sources with direct knowledge told Reuters, nearly three years since deals with the world's largest independent energy trader were banned over a graft scandal.

The ban followed Swiss-based Vitol's public acknowledgement in December 2020, in a deal with the U.S. Department of Justice, that it had paid kickbacks to win business with Pemex, as well as state companies in Brazil and Ecuador.

In recent days, two vessels carrying Vitol cargos arrived at two Mexican ports, two sources familiar with the deals told Reuters, speaking on the condition of anonymity because the information was both commercially and politically sensitive.

A third senior trading source confirmed that Vitol had resumed business with Mexico.

Neither the deals nor the fact that Mexico resumed trading with Vitol have previously been reported.

Vitol declined to comment while Pemex and the Mexican government did not respond to requests for comment.

Liberia-flagged vessel Arvin had set sail from Houston on Sept. 7, partially loaded, bound for the Mexican port of Pajaritos, LSEG data showed. It arrived in Pajaritos two days later and finished discharging on Sept. 15.

Meanwhile, Denmark-flagged vessel Torm Thames finished discharging on Sept. 13 at the Mexican port of Tuxpan and moved empty to nearby Tampico, where it is moored, LSEG data showed.

Port records showed Arvin carried regular gasoline and methyl tert-butyl ether, or MTBE, an additive for unleaded gasoline that increases octane and oxygen levels and reduces pollution. Torm Thames carried premium gasoline and MTBE.

Reuters was unable to determine the terms of the settlement between Mexico, one of the world's largest importer of refined oil products, and Vitol.

Mexico's President Andres Manuel Lopez Obrador and Pemex CEO Octavio Romero had both publicly said the country would only resume dealing with Vitol if adequate compensation was paid and the company handed over the names of those involved in the graft scandal.

Pemex later disclosed the names of two former officials and said that Vitol offered compensation but it was not clear how it was settled.

In the wake of the graft scandal that roiled Latin America, Reuters reported that Mexico was looking to renegotiate some of its hundreds of millions of dollars-worth of contracts with the Geneva-based company.

Pemex's Romero had said the company would jettison terms it considered unfavorable. Eventually, Pemex officials pulled the plug on contract negotiations after Vitol officials refused their proposed changes to terms.

It was unclear when negotiations restarted.

Meanwhile, legal proceedings in the U.S. continue.

In late August, Javier Aguilar, a former manager for an affiliate of the Vitol group of companies, appeared in Houston federal court, records showed.

The court records showed he appeared in court on Aug. 21, pleaded not guilty and was released on a $100,000 bond.

He is alleged to have conspired to violate the anti-bribery provisions of the Foreign Corrupt Practices Act (FCPA) and violate the FCPA, the Travel Act and the money laundering statutes in connection with a scheme involving Mexican government officials.

Aguilar was first indicted on Sept. 20, 2020 by a federal grand jury in Brooklyn on charges of scheming to bribe Ecuadorian officials on behalf of Vitol, his employer. He pleaded not guilty.

He is set to go on trial in the Ecuador case in January.

A second indictment in Brooklyn on Dec. 2 last year, added charges related to a separate scheme to bribe Mexican officials on Vitol's behalf, but those charges were dismissed on May 31 due to a lack of appropriate jurisdiction.

Similar charges stemming from the alleged bribery scheme in Mexico were filed in Houston on Aug. 3.

(Reporting by Stefanie Eschenbacher and Ana Isabel Martinez in Mexico City and Dmitry Zhdannikov in London Additional reporting by Luc Cohen in New York, Marianna Parraga in Houston and Florence Tan in Singapore Editing by Stephen Eisenhammer and Marguerita Choy)