The plans for the Monastery of Studios, which was dedicated to St John the Baptist and was considered the most important of Constantinople, were revealed by the Hurriyet Daily News.
Religious authorities in the city could not immediately be reached for comment on the report, which comes amid increasing criticism of the government over its attempts to impose Islamic values on secular society in Turkey.
Two churches of the same name in other parts of Turkey have recently been turned into mosques, adding to the estimated 83,000 across the country.
Hurriyet said the monastery, which has been left in ruins by fire and earthquakes with only part of the church remaining, would be restored next year and then converted.
Hagia Sophia, now one of Istanbul's most popular tourist attractions, was a church for centuries -- and the seat of the Patriarchate of Istanbul -- before the Ottomans turned it into a mosque in the 15th century.
Debate about the role of religion in Turkish society has intensified in the run-up to a highly-charged election period, kicking off next March with local polls.
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