Bulgarian crime writer Georgi Stoev was murdered in April this year
The European Commission has suspended EU aid to Bulgaria worth hundreds of millions of euros because of concerns about corruption and organised crime.
Commission spokesman Johannes Laitenberger said the EU was also withdrawing the right of two Bulgarian agencies to manage EU funds.
Bulgaria's PM admitted his country had not done enough to meet EU standards.
Romania was also criticised for shortcomings in its judiciary, including politicisation of cases.
Romania will escape penalties for now, but its report says the reforms remain "fragile".
About 500m euros (£400m; $800m) of aid to Bulgaria is being frozen by the commission.
"The truth is Bulgaria is learning how to manage EU funds," Bulgaria's Prime Minister Sergei Stanishev said in reaction to the reports.
He acknowledged that "there is a discrepancy between the political will, which is a fact, and the achievement of concrete results".
Both countries have been under close supervision since they joined the European Union in January 2007.
In Bulgaria, "the fight against high-level corruption and organised crime is not producing enough results," Mr Laitenberger said, presenting the reports on Wednesday.
In the toughest terms ever used about a member state, the EU executive says that despite some efforts to fight corruption and organised crime, Bulgaria's "institutions and procedures look good on paper but do not produce good results in practice".
One of the series of reports published on Wednesday condemns "a lack of commitment to act swiftly and decisively when fraud is identified", and refers to "a strong suspicion of the involvement of organised crime".
The reports describe a "growing sense of frustration" among other EU countries who have sent experts to support Bulgaria.
Mr Laitenberger said Bulgaria needed a new penal code to ensure more effective justice.
However, after strong lobbying from the Bulgarian government, the report was toned down to some extent, the BBC's Oana Lungescu reports.
A warning that corruption allegations could delay the country's admission to the Schengen passport-free area and the eurozone was removed.
Mr Laitenberger said the commission was prepared to lift its suspension of funds "as soon as Bulgaria has taken the necessary corrective measures".
Meanwhile, the opposition in Bulgaria is pushing for a no-confidence vote in the Socialist-led government.
The report on Romania condemns parliament for delaying corruption inquiries involving the former Prime Minister Adrian Nastase and other top officials.
It also calls on Romania not to adopt legal changes that would make it much harder for prosecutors to search the homes and wire-tap the phones of corruption suspects.
Romanian Prime Minister Calin Popescu Tariceanu welcomed the report, saying it would motivate Romania to speed up reforms.
While praising the "consistently good record" of Romanian prosecutors, the European Commission notes that in 90% of corruption cases, lenient judges deliver the minimum penalty.
But the Commission is no longer in a mood for leniency, our correspondent says.
Jacki Davis from the European Policy Centre in Brussels says there is a clear message to Bulgaria and Romania, but also for EU candidates, from Croatia to Turkey.
"Negotiating the terms of your EU membership isn't the end of the story. If you make promises, you have to live up to them. So it's shape up or face sanctions," she says.