Dougie Hall replaces Scott Lawson at hooker, while Alastair Kellock makes his RBS 6 Nations debut at lock in place of Craig Hamilton.
But Hadden admits the choice of scrum-half had been a difficult one.
He said: "We are in a most fortunate position to have some real talent there and, as ever, it was a close call.
"Mike will start against France because he's in good form.
"He came on for Chris in the game against New Zealand and did well, so deserves a start.
"It is very much a case of horses for courses and I am sure that Chris will have an opportunity at some point in the championship."
Hadden is also confident Hall and Kellock will contribute well against the French in the pack.
He added: "There's tremendous competition at hooker where Ross Ford is also hammering on the door.
"We monitored Dougie exceptionally closely during the autumn Tests and he starts in front of Scott Lawson on this occasion.
"Alastair Kellock has been a key figure for Edinburgh this season.
"He has nudged himself up the pecking order and is maturing into a powerful and athletic second row."
The Scotland boss insisted the selection of stand-off Dan Parks was an easier choice after his displays in November.
Hadden said: "Dan compared most favourably to the three stand-offs he was up against in the autumn."
Scotland captain Jason White will celebrate his 50th cap leading the team for the first time in the RBS 6 Nations.
The Sale Sharks back-row forward took the captain's armband for the first time for the three Tests in November.
Hadden said: "It's a fantastic milestone for Jason and I congratulate him on becoming the 20th Scot to win 50 or more international caps.
"It's a mouth-watering prospect playing against arguably one of the top two sides in the world, particularly after we played against one of the other top sides in the world in our last game.
"The challenge for us is to see what progress we have made since then."
Scotland team to play France in the RBS 6 Nations on Sunday, February 5 at Murrayfield:
H Southwell (Edinburgh Gunners); C Paterson (Edinburgh Gunners), M Di Rollo (Edinburgh Gunners), A Henderson (Glasgow Warriors), S Lamont (Northampton Saints); D Parks (Glasgow Warriors), M Blair (Edinburgh Gunners), G Kerr (Leeds Tykes), D Hall (Edinburgh Gunners), B Douglas (Border Reivers), A Kellock (Edinburgh Gunners), S Murray (Edinburgh Gunners), J White (Sale Sharks), S Taylor (Edinburgh Gunners); A Hogg (Edinburgh Gunners).
Substitutes: S Lawson (Glasgow Warriors), C Smith (Edinburgh Gunners), S MacLeod (Border Reivers), J Petrie (Glasgow Warriors), C Cusiter (Border Reivers), G Ross (Leeds Tykes), S Webster (Edinburgh Gunners).