Mueller is using the trove to confirm existing information and open up new leads in his widening inquiry, according to Axios.
The emails reportedly include conversations about sensitive topics, such as policy planning, potential appointments and the political views of senators involved in the confirmation process.
A lawyer for Trump’s transition team, Kory Langhofer, claimed Mueller has obtained the emails unlawfully.
Langhofer sent a seven-page letter to House and Senate oversight committees, raising potential violations of the Fourth Amendment of the US Constitution, which protects against unlawful search and seizure.
The attorney said the special counsel’s office acquired the records from the General Services Administration, a federal agency that holds all transition materials, earlier this summer.
Langhofer argued that Mueller’s team of prosecutors has “extensively used the materials in question” even though they knew some of the materials were subject to attorney-client privilege and other protections.
"We understand that the special counsel's office has subsequently made extensive use of the materials it obtained from the GSA, including materials that are susceptible to privilege claims," Langhofer's letter said.
Legal experts pushed back on the claim that Mueller obtained the emails unlawfully
"Of course Mueller obtained emails from a third party," said federal prosecutor Renato Mariotti, according to Business Insider.
"Prosecutors in most white collar criminal investigations do that. It's not 'inappropriate' or even unusual. Anyone who claims otherwise has no idea what they're talking about," he added.
The emails in question could shed light on critical events during the transition period last year, which have now become the focus of the Russia investigation.
Some of the emails belong to Jared Kushner, Trump’s son-in-law who is now his senior adviser.
They reportedly include Kushner’s meeting with a Russian banker with close ties to Russian President Vladimir Putin as well as a meeting between Kushner and the Russian ambassador, Sergey Kislyak, which was also attended by then-National Security Adviser Michael Flynn.
Investigators could use the emails to connect the dots on the events pertaining to Flynn's conversations with Sergey Kislyak — which he would later mislead FBI agents about during a January 24 interview.
Early this month, Flynn pleaded guilty to lying to FBI agents about his interactions with the Russian ambassador. He has agreed to cooperate with Mueller’s investigators as part of a plea bargain.
Trump said in a tweet that he fired his former national security adviser in February “because he lied to the vice-president and the FBI.”
The tweet sparked a firestorm of criticism as it showed the president knew Flynn had committed a serious crime at the time when he pressured former FBI Director James Comey not to investigate him.