The prime minster’s close ally Darren Jones sent his commiserations to Peter Mandelson after he was sacked as US ambassador in messages that were not disclosed as part of the humble address release.

Jones’s texts also included requests for advice on the reshuffle and disobliging comments about the then business secretary Jonathan Reynolds and the influence of trade unions.

The chief secretary to the prime minister was one of the ministers who said they had nothing to release because they had previously deleted messages or changed phones.

Mandelson, who was sacked last September because of revelations about his close friendship with the late sex offender Jeffrey Epstein, declined to hand over his own messages. The release of the files was prompted by a parliamentary motion that demanded the mass release of government communications relating to Mandelson.

In the messages, reported by the Spectator, Jones wrote to Mandelson: “You’ve been doing such a great job, and you worked wonders with Trump. I’m so sorry about today.”

In a previous message, Jones, then chief secretary to the Treasury under Rachel Reeves, told Mandelson that it did not “fill you with confidence” that Reynolds and the former deputy prime minister Angela Rayner were in charge of the government’s growth plans along with Reeves.

He also reportedly said he had “lost faith” in Reynolds’ advisers “when, on a call about Port Talbot, they repeatedly took a different position to us in HMT ‘because that’s what the unions want’.”

According to the report, Jones also requested “thoughts/advice” about a proposed reshuffle and said he hoped to be appointed business secretary, technology secretary or energy secretary. He also said: “I also like MoD but think that’s unlikely.”

“DBT [Department for Business and Trade] my preference – everyone fond of Jonny but perception that DBT not firing on full cylinders,” he wrote.

Jones is understood to have replaced his phone after he began his role at the Cabinet Office and took over responsibility for cybersecurity.

In a pointed comment on Wednesday night, he told MPs that only Mandelson would be able to disclose any messages between the two of them.

“The only person who could release those messages, if they had them, would be Peter Mandelson, who has refused to disclose his phone to the process,” he said.

Starmer is also previously reported to have texted Mandelson with a warm message that did not appear as part of the humble address release.

The Spectator reported he had written to the former ambassador upon his appointment saying: “You’ll be brilliant in challenging circumstances. And after many years of discussions, we get to work side by side. I really look forward to that.”

Jones told parliament on Monday that the Cabinet Office accepted there were messages that could not be retrieved. “Members should note some messages may not have been backed up where devices may have been changed, or disappearing messages were turned on, for reasonable and permitted reasons – including before the dismissal of Peter Mandelson or the passing of the humble address – myself included.”

More than 1,500 pages of documents were published by the government on Monday afternoon, which the government said was “an unprecedented piece of government transparency”. However, MPs and others have raised questions about missing documents – some of which have been withheld because of a police investigation into Mandelson for misconduct in public office.

Jones has said the documents will be published when the police deem it is no longer prejudicial to their inquiry.

The prime minister’s former chief of staff, Morgan McSweeney, told a foreign affairs select committee inquiry that he had exchanged messages with Mandelson on the day of the reshuffle, shortly before Mandelson was dismissed. Those messages have not yet been disclosed.

McSweeney is also said to have sent questions to Mandelson about his relationship with Epstein. That note, as well as Mandelson’s responses, did not appear in the second tranche of documents.

Also missing was a nine-page summary document produced by United Kingdom Security Vetting (UKSV), outlining areas of concern over Mandelson’s security clearance. Their initial advice was overruled by the Foreign Office’s then permanent undersecretary Olly Robbins.

Speaking in the Commons on Wednesday, Jones said he wanted to apologise to MPs and to Epstein’s victims for the fact that, he believed, he personally had benefited from knowing Mandelson. “I want to take the opportunity to ask myself questions about my relationship with Peter Mandelson,” Jones said.

While he said he did not ignore concerns about Mandelson’s appointment – because none were raised – he said he had acted a certain way around Mandelson because he perceived him to be influential.

“Did I at best treat Peter Mandelson differently because I perceived him to have influence and power in the Labour party? I think the answer to that is yes, I did. Have I benefited from that relationship? I think in part the answer to that is yes. And for that I would like to apologise to the house, the victims … and commit to doing something about it.” He said he would like to meet victims of Epstein, “if that were appropriate”.