Atapattu has not played since March because of an acute disc problem in his lower back but had hoped to return for the two Tests against South Africa and a one-day Tri-Series also involving India in August.
The 35-year-old travelled to Australia in May for surgery on the career-threatening injury but the rehabilitation process has been slower than expected.
"Marvan needs time to rehabilitate and strengthen his back," De Mel told journalists.
"He is very eager to get back on the field but we do not want to rush him back into the team until he is 100 percent fit," he added.
"We have had a chat together and have decided to target the ICC Champions Trophy in October."
Atapattu has been a cornerstone of the Sri Lankan top order for a decade, scoring 5,330 runs in 88 Tests and 8,233 runs in 253 one-day internationals.
Mahela Jayawardene, Atapattu's stand-in during the recent tour to England, has been reappointed captain for the Test series against South Africa and the one-day tournament.
The selectors have also picked 20-man training pools for both series, the names of which will be released next week.
The players are due to resume full training on Thursday after a short holiday to recuperate from a 10-week tour of England and the Netherlands.
