Wayne Rooney feels he got "slaughtered" for his display in last month's win in Slovakia after former England boss Sam Allardyce stated that his captain "played wherever he wanted".
The 30-year-old, who has played mainly as a forward, operated in a deeper role for much of the 1-0 win in Trnava.
Rooney revealed that Allardyce, who lost his job last week, admitted to him that his comments had been a mistake.
"I played exactly to instructions," said the Manchester United player.
"He knew he had made a mistake. He said that to me on the plane home.
"That's part of being involved at this level. He understood that quite early and unfortunately he doesn't have the chance to rectify that now."
Rooney, England's all-time leading scorer with 53 goals, also thought he had given "a decent performance" against Slovakia.
England won their opening World Cup 2018 qualifier 1-0 thanks to an injury-time winner from Liverpool's Adam Lallana.
"I actually thought I'd done quite well, especially in the second half," said Rooney. "It has all been blown up."
Allardyce left his post as England manager by mutual agreement with the Football Association last week after only one match and 67 days in charge.
It followed a newspaper investigation claiming he offered advice on how to "get around" rules on player transfers.
"It's a shame," said Rooney. "Everyone could see how excited Sam was for the job and he came in and showed that enthusiasm to the players.
"It's a shame it's happened and I'm sure he deeply regrets it. For the FA, I'm sure it has been a tough couple of weeks."
Gareth Southgate will take charge of England for the next four games.
Rooney thinks it's an opportunity for the England Under-21 boss to "show what he can do at senior level".
"We have to buy into his ways and take his ideas on board," said Rooney.
Rooney's place in the England side has been under scrutiny since the country's failure at Euro 2016, where he played in midfield.
Asked where he thought he would play for England under Southgate, Rooney said: "It is getting tiring, that question. I have answered it many times.
"It is the same answer. I will play where the manager wants me to play. I have never picked myself."
On Monday, Southgate confirmed that Rooney will remain as captain, describing the forward as "the outstanding leader in the group".
Rooney welcomed the backing of the interim boss, saying: "With Sam, there was a lot of talk over whether I would be captain. It was good Gareth put that to bed early and there was no unnecessary speculation."
Cahill looking to correct errors
Gary Cahill is expected to start in the centre of defence against Malta.
The 30-year-old has made some high-profile mistakes for Chelsea in recent weeks, including against Swansea when he allowed Leroy Fer to rob him of possession and score the equaliser.
"Up to Swansea, my form was good, I was playing well and I was happy," Cahill told BBC Sport. "But since then I have made a few big errors, basic errors. As ridiculously bad as they were, they are easy to correct."