Justice Minister Sabine Leutheusser-Scharrenberger called for the states to put in their share of the money, while victims' groups said they were bitterly disappointed at the results so far.
The government set up a "round table" group of representatives from the federal and state governments as well as victims groups to come up with recommendations of what to do after numerous cases of abuse were revealed from around the country.
A major recommendation was to set up a €100 million compensation fund - the cost of which would be shared between state and federal governments. But all the state governments apart from Bavaria have said they could not make their contributions, saying there was no overarching concept for how the money would be distributed.
Leutheusser-Scharrenberger rejected the claims, and said the federal government would pay its share and start operating the fund.
She also on Wednesday presented a new draft law designed to improve victim protection - a draft that has been hanging in limbo for the past 20 months as state and central governments scrapped over who should pay for what.
“We have to do everything we can to make sure that the urgently needed help for child sex abuse victims can be freed up,” she told the Wiesbadener Kurier regional newspaper on Wednesday.
Matthias Katsch, speaking for the victims said that the government should first begin paying out compensation from the €50 million in the fund.
Katsch added that the fact victims have had to wait nearly three years since the round table was set up for compensation was a source of “great anger.”