Todd told BBC Spotlight he does not think former England striker Mariner will see the move as a demotion.
"Paul is in the job that he was brought in for, and this has been done all cards face up on the table," he said.
"If Paul was here with us he would say exactly the same thing, that he was head coach and that was what he was brought in for."
Investing in a experienced proven manager is an important piece of the jigsaw.
Keith Todd
Mariner initially joined the Pilgrims in October 2009, when he was brought in to work alongside manager Paul Sturrock.
When Sturrock was relieved of first-team duties in December, Plymouth's board handed Mariner the reins, giving him responsibility for all footballing matters.
Todd said: "We asked him to take the lead through to the end of the season, probably earlier in his career in the UK in management that we or he may of perfectly planned on.
"Paul Mariner has brought a new vitality to the team, but it's a hard world, a results driven world and it wasn't quite enough."
Todd also addressed concerns that Argyle would struggle to afford a new boss alongside existing coaches Mariner and John Carver.
"I'm not going to deny that they'll be a net additional cost," said Todd.
"But in the realms of the total budget I think we regard it as an investment in the future then in businesses you have to decide where you invest and we concluded that investing in a experienced proven manager is an important piece of the jigsaw."
Source: BBC Sport
Source: BBC Sport