Gareth Southgate has said he is unafraid of dropping Wayne Rooney and showing the tough streak the England caretaker manager once had to employ at Middlesbrough, where he recalled “making some really close friends redundant” after the club had been relegated under his stewardship.

Southgate drew on those memories, describing it as one of the more difficult experiences of his professional life and “probably as big as you can get” to highlight he would be willing, if necessary, to leave out Rooney at a time when England’s record scorer is struggling for form and has lost his place at Manchester United.

However, he also gave Rooney another vote of confidence after a section of the Wembley crowd briefly booed the England captain in Saturday’s 2-0 win against Malta. Southgate’s belief is that Rooney’s importance to the squad is not fully understood outside the England camp and there was no clear indication of the player being removed from the side for ’s game in Slovenia.

“I think he commands that respect,” Southgate explained. “When he makes his observations and he speaks up, it’s clear that he talks with authority but also insight. His knowledge is of a very high level, not just of the game but the dynamics of the group and the things they can learn and improve upon. It’s impossible to feel that really unless you are inside it.”

He opted to play Rooney alongside Jordan Henderson as the central midfielders in a 4-2-3-1 formation against Malta but now wants Eric Dier to return to the starting line-up. Dier was left out against Malta because he has had hamstring problems and England’s management did not think it was right to involve him twice in four days.

Rooney has not started any of United’s last three matches but Southgate described himself as “very pleased” with the player’s performance against Malta. “I think at this moment in time that’s irrelevant,” Southgate said, in response to questions about Rooney’s reduced role at Old Trafford. “We’ve got 30% of the Premier League eligible for England. Of that, some don’t want to play [for England]. Some aren’t good enough to play and we’ve got a captain who is desperate to lead on and off the field and continues to make an outstanding contribution to that group of players. That was why he was selected. What’s happening at Manchester United, for this week, is not as important.”

Southgate did, however, say that “the longer a situation goes where you are not playing with your club, it becomes more difficult” and, with three games remaining in his spell as caretaker manager, he bristled to a question asking if he would dare remove a player of Rooney’s status. “I’ve got to make decisions which are right for the team and, whenever you select a team for England, you’re going to leave out some players. You look at the bench [against Malta] and there are guys who are playing every week in the Premier League, so you have to be prepared to do that (make tough decisions). That’s part and parcel of the job.”

The England squad fly out on Monday and Jordan Pickford, Sunderland’s 22-year-old goalkeeper, has been called-up after Tom Heaton pulled out with a minor injury.