Flintoff is on course to play again as a specialist batsman in Lancashire's next game, against Worcestershire in the County Championship on Wednesday, as long as he is given the green light by the England management.
"We'll look at the situation on Tuesday and take it from there, but if we have orders from on high not to play him then obviously we won't. He won't play any cricket before he's ready for it," added Watkinson.
Flintoff will be happy to have come through his first game of the season, coming 85 days after a bone spur was removed from his left heel.
Looking a shade trimmer after a gruelling rehabilitation regime of pounding the hills near his Preston home, the all-rounder had a quiet game which nonetheless qualified as a satisfying workout.
Unable to bowl, he was rarely required in the field and it wasn't until 5.16pm that he was given his first meaningful action in what promises to be the most significant summer of his career so far.
Coming in to bat at number five with Lancashire struggling on 46 for three in testing conditions, he was given an excellent reception by a healthy crowd of nearly 3,000.
Flintoff began circumspectily before getting off the mark on the 10th delivery he faced with a heave for four off Middlesex debutant Scott Styris.
A couple of sweetly timed ondrives followed, as well as a few play-and-misses before he was adjudged lbw to Styris playing across the line to a delivery that ducked in and kept a little low. His 17 had come off 23 balls in a 34-minute stay at the crease.
Perhaps most significantly he was able to sprint one quick single and showed no ill effects from the operation he underwent in early February.
But he was unable to prevent Lancashire slipping to a 69-run defeat to Middlesex after the home side recovered from 37 for six to post 210 for nine off their 45 overs. James Dalrymple top scored with a classy 81 off 82 balls.
Surrey's indifferent start to the season continued. They are rock bottom of Division Two after being bowled out for 86 at the Riverside, where they lost to Durham by 138 runs.
