Prasad was speaking a day after the India selectors decided to drop veteran batsman Yuvraj Singh from the squad for five ODIs and one T20I to be played in Sri Lanka.
The 35-year-old Yuvraj was axed after not scoring a half-century in his last six innings with the selectors also bringing in younger players as they look towards the 2019 World Cup.
Dhoni, who is 36, retained his place in the squad for the Sri Lanka series but Prasad made it clear that the 2011 World Cup winning skipper is no longer an automatic choice behind the stumps.
Asked if Dhoni’s place had been discussed, Prasad said: “Discussions happen about everybody. It is not just MS. When we pick, when we talk about combinations, we talk about everybody. You will also see in time to come.
“We don’t say it is an automatic this thing… but we will see. We are all stakeholders. We all want the Indian team to do well.
“If he is delivering, why not? If he is not, we will have to look at alternatives.”
The first ODI between India and Sri Lanka is set to take place in Dambulla on Sunday.