Distin injured his hamstring in last weekend's win over Manchester United and he is likely to miss the clash with Southampton on Saturday.
Jagielka has been out with a similar injury since the end of February and Martinez insists he will not return to his first-team plans until he is 100% ready to do so.
If both miss the Southampton match, Martinez will be down to youngster John Stones and little-used Antolin Alcaraz as his centre-back options.
"Phil Jagielka has got his own programme and it is important that we follow that and we don't rush him back," he told evertontv.
"He has been involved with the first-team training now and that is a really good sign.
"We want Phil back as quick as we can but not because we have got an injury with Sylvain.
"We aren't going to rush and do the wrong things in his individual programme.
"Phil is going to be fully fit very soon and I do expect that he will probably be able to make the squad against Manchester City (on May 3) and that's always been the plan.
"I do believe that we will be able to reach that."