In a joint statement from police and the public prosecutor's office on Saturday, Schaefer - who led the finance ministry of Hess for nearly a decade - was found dead next to railway tracks near Frankfurt.
A German provincial Finance minister, who was reportedly anxious about the financial impact of the coronavirus pandemic, has been found dead, having allegedly committed suicide, reports said on Sunday.
Hesse is one of the wealthiest states in Germany and home to Frankfurt am Main, which is regarded as the financial capital of Europe's largest economy.
Thomas Schaefer, 54, the finance minister of Hesse state, Germany, was found on a high-speed train line in the town of Hochheim between Frankfurt and Mainz, the police confirmed on Saturday.More news: Iran COVID-19 Death Toll Tops 2,500
Like Bouffier, Schaefer belonged to Merkel's centre-right CDU party.
Thomas Schaefer was immensely popular among his colleagues and he was touted as a possible successor to Bouffier.
Schaefer, an active member in the Hessian state politics for more than two decades, had been the Finance Minister of the state for almost 10 years.
'I have to assume that these worries overwhelmed him, ' Mr Bouffier said.More news: Woman in her 70's confirmed to be NZ's first COVID-19 fatality
Bouffier recalled in a statement how Schäfer worked "day and night" to provide help to the companies and workers tackle the economic impact of coronavirus outbreak.
Schaefer is survived by his wife and two children.
Germany's federal and state governments have drawn up huge aid packages to cushion the blow of largely shutting down public life to slow the spread of COVID-19.More news: Joe Diffie Dies At 61 From Complications From Coronavirus