The judge who will oversee the January antitrust trial of Thomas Farmer is poised to consider allegations by lawyers of the former Crowley Maritime Corp executive that US authorities ruined a valuable piece of evidence.

District judge Daniel Dominguez, of the US federal court in Puerto Rico, has called for a hearing to consider the claim that so-called “conspiracy journals” kept by two key witnesses for the prosecution’s case have been severed from their bindings and reordered, and sections have gone missing.

And it has emerged that the alleged spoliation did not take place at the hands of the two alleged co-conspirators, as government lawyers said for months. Instead, prosecutors now say the journals were taken from their bindings on the authorisation of an agent with the Federal Bureau of Investigation (FBI).

Farmer, a former vice-president of price and yield management for Crowley Liner Services, who has pleaded not guilty, faces charges that he was part of a conspiracy among three US containership owners to fix prices and allocate customers on the Jones Act-protected trade lane between the US mainland and Puerto Rico.

The conspiracy, which took place between 2004 and 2008, allegedly involved Crowley, Horizon Lines and Saltchuk Group-controlled Sea Star Line, which have all paid out fines.

The trial is set to begin 26 January in San Juan, Puerto Rico’s capital.

Two key witnesses against Farmer are former Horizon marketing and pricing director Gregory Glova and former Sea Star executive Peter Baci, who both pleaded guilty and were sentenced to prison terms.

In a trial against former Sea Star president Frank Peake early this year, the two witness claimed to have used handwritten journals throughout the price-fixing conspiracy. Peake is currently appealing his five-year prison sentence.

In April, as a member of Farmer’s legal team was examining the records in preparation for the trial, he discovered that they were removed from their bindings and reassembled out of sequence, in addition to the fact that certain periods were missing.

Prosecutors later said Baci and Glova were responsible for the alterations to the journals but they then acknowledged last month that an FBI agent hired a contractor to make electronic copies of documents used in the criminal investigation.

The US Justice Department lawyers argue that the arguments by Farmer’s team are meritless, since an affected party must be involved in altering evidence for a spoliation claim to succeed. Plus, they argue that it is pointless to challenge the evidence now that they do not plan to use the journals against Farmer at trial.

But Farmer’s legal team have argued that reviewing the journals, which include the entire time period of the alleged conspiracy, could have key evidence for the shipping executive’s defence.

“If this were the pages to Don Quixote, it would be one thing,” wrote lawyers for Farmer in court records. “These are, according to the government and its witnesses, the handwritten chronicles of the conspiracy from the perspective of its managers at Sea Star and Horizon, spanning years. They are irreplaceable.”