"The act of abandoning one's religion is a sin punishable by God on the Day of Judgment. If the case in question is one of merely rejecting faith, then there is no worldly punishment," he wrote.
In many Muslim societies, those who convert to another religion are considered apostates and can be subject to capital punishment.
Gomaa said that if the conversions undermine the "foundations of society" then it must be dealt with by the judicial system, without elaborating.
Attempts by Muslims in Egypt to convert to other religions have been hindered by the state's refusal to recognize the change in official documents and in some cases have led to arrests and imprisonment.
"Even though it is not a criminal offense in Egypt, they get detained under emergency laws or are put on trial for contempt of religion if they wish to convert," said Hossam Bahgat of the Egyptian Initiative for Personal Rights. "This [ruling] is significant, especially coming from Gomaa," he added.
"Between 2004 and now there have been many court cases involving Christian converts to Islam that want to convert back to Christianity who are unable to do so."
Bahgat, who is involved with a case of 12 former Christians who converted to Islam and are now trying to revert, said that Gomaa's previous fatwas on the issue said that apostasy threatened public order.
The current opinion opens the possibility of converting without threatening "the foundations of society."
A spokesman for Dar Al Iftaa, the body headed by Gomaa that is responsible for issuing religious opinions, maintained that the mufti's stance has not changed.
"The posting is consistent with the mufti's past fatwas," he said. "Apostasy is only punishable when it is considered akin to subversion."
The issue of apostasy is a thorny one in the Islamic world, with one extremist interpretation declaring that apostates should be killed.
"The punishment for apostasy is controversial," Judge Ahmed Mekky, the deputy head of Egypt's supreme court, said. "There is nothing in any Koranic text about this."
Instead the texts talked about apostates who were put to death for treachery - a political rather than religious crime.
The case of the 12 Copts, whose request to revert was denied by a lower court in April, goes in front of the supreme court in September, and Bahgat said that they will use Gomaa's posting to bolster their case.
"Gomaa is a civil servant, the top religious advisor of the state, and technically speaking the deputy minister of justice," he said. "So his views on the matter carry authority