The full-back, who is returning to play for Wigan in 2016, has withdrawn from the Test series against New Zealand due to a knee problem.
But the England coach has also insisted that the decision to include Tomkins in the squad was justified, with the evidence which was available to him and his backroom team.
Tomkins had been training fully with the squad, until he suffered a negative reaction to a Tuesday training session.
“I’m happy with the cover we’ve got,” said McNamara.
“We’ve got a fair bit of depth throughout the squad. We feel we’ve got most positions covered.
“He [Tomkins] had a pretty strong reaction to the session after Tuesday.
“All of the information that we were given was that if you strengthened the knee to a certain level, there was a strong possibility that he would be able to play in this Test series, and that he would be fit for the first Test.
“With those odds, we took the opportunity to include him in the squad.”
McNamara maintains that Tomkins has been a valued member of the group, who remains totally commited to the England cause.
“He’s done a brilliant job,” he added.
“He’s worked so, so hard. He really has strengthened his knee.
“There’s no issue in terms of the strength of the knee, but there’s an underlying issue there that unfortunately reacted after the tough training session that he went through.
“He’ll have to go back and seek further opinions now in the next few weeks.
“Anyone who knows Sam knows that he’s passionate about playing for his country. He was extremely determined to be available for this Test series.
“He pushed himself to the limit in terms of getting himself ready to play.
“It’s a pretty big blow for Sam. We’re disappinted as a squad that we’ve not got Sam available for selection.
“It’s a little bit of a blow to us, but it’s a bigger blow for Sam, he was desperate to play.
“We get to move on, we get to play. Unfortunately for Sam, he has to sit and watch from the sidelines.”