FBI Director James Comey distrusted former Attorney General Loretta Lynch because he believed she helped play down the investigation into Hillary Clinton's private server, according to a new report.

Comey ended up plunging the FBI into the center of the 2016 presidential election when he reopened the investigation into Clinton's emails just weeks before the election.

The New York Times revealed that Comey handled the investigations into Clinton and Donald Trump, very differently.

According to several government officials, Comey rewrote the script when it came down to the Clinton case, mainly because the FBI believed she would win the election and feared they would be accused of helping her.

In Trump's case, Comey did everything by the book, with the FBI's traditional secrecy, according to the Times.

FBI Director James Comey (left) distrusted former Attorney General Loretta Lynch (right) because he believed she helped play down the investigation into Hillary Clinton's emails, according to a new report by the New York Times

The Times report also revealed that Lynch did not want Comey to send a letter to Congress about the discovery of new emails relating to the investigation into Clinton’s private server before the November election

It is claimed this master plan, which the Times has called a 'go-it-alone strategy', stemmed from Comey's distrust of senior officials at the Justice Department, including his boss, Lynch.

Comey and other FBI officials felt Lynch and other in the Justice Department had provided Clinton with political cover, according to the Times.

During a meeting in September 2015, Lynch reportedly called on Comey to use the word 'matter' instead of 'investigation' when publicly discussing the Clinton case, three officials told the Times.

According to the newspaper, Lynch reasoned that the word 'investigation' would raise a number of other questions.

She also reportedly argued that the department should maintain its policy of not confirming investigations.

Shortly after the investigation was opened against Clinton, the Justice Department confirmed to reporters that it had received a criminal referral, a step toward a criminal investigation.

But the next day, the department revised its statement, saying it was 'not a criminal referral'.

'The department has received a referral related to the potential compromise of classified information,' the new statement read.

In reality, agents had already been alerted to mishandled classified information and had opened a full criminal investigation, despite what officials said in public.

Authorities within the FBI also suspected that Democratic appointees were playing games to help Clinton, who immediately released a statement reiterating that it was 'not a criminal investigation', but a 'security review', according to the Times.

In a separate probe, Comey sent a letter to Congress and informed lawmakers that emails had been discovered in connection with Rep Anthony Weiner (left in 2013), who is married to longtime Clinton aide Huma Abedin (right)

The FBI announced that it had found no information to change its initial conclusion to not bring charges against Clinton (pictured in April 2017), just days before the election

After Clinton's shocking defeat against Trump in the presidential election, she and her aides blamed the FBI and Comey as one reason why they lost

Lynch then came under pressure to recuse herself from the investigation entirely after she had a discussion with former President Bill Clinton in June 2016.

However, Lynch did not recuse herself, but the situation did lead her to say she would accept whatever conclusions career prosecutors and the FBI reached, according to the Times.

The Times report also revealed that Lynch did not want Comey to send a letter to Congress about the discovery of new emails relating to the investigation into Clinton’s private server before the November election.

Lynch was 'stunned and confused' to hear that Comey was planning to send the letter just weeks before Election Day, according to the newspaper.

Aides for Lynch talked to Comey's staff about putting off the decision, according to the Times, and Lynch could have ordered Comey against sending the letter.

However, her aides advised her not to because if Comey refused, Lynch could have been put in the position of having to fire him, the Times reported.

Comey's letter went straight to Congress and informed lawmakers that emails had been discovered in a separate FBI probe into former Rep Anthony Weiner, who is married to longtime Clinton aide Huma Abedin.

The FBI announced that it had found no information to change its initial conclusion to not bring charges against Clinton, just days before the election.

After Clinton's shocking defeat in the presidential election, she and her aides blamed the FBI and Comey as one reason why they lost.