1128 GMT February 22, 2020
The commission plans closer monitoring of those schemes and of "golden visas" granting residence in exchange for big investments, BBC wrote.
It says they can be abused for tax evasion and money-laundering.
EU citizenship gives an individual free movement in most of the EU, easy access to the single market and other rights.
Twenty EU countries have such schemes.
Cyprus, Malta and Bulgaria give passports to non-EU nationals who make sufficient investments in their countries. Rich foreigners can buy passports there for between €1 million (£870,000; $1.1 million) and €2 million.
They and 17 other EU member states, including the UK, also grant residence rights to investors. That right puts an individual on the path to citizenship.
In a new report the commission said there is not enough information about how the schemes work. It is setting up a special team to monitor the schemes and boost information-sharing.
The anticorruption campaign group Global Witness said the EU had raised the alarm but not offered solutions, the BBC's Adam Fleming reported from Brussels.
In a report last October, another anticorruption group, Transparency International, said Spain, Hungary, Latvia, Portugal and the UK had granted the most golden visas to investors and their families, ahead of Greece, Cyprus and Malta.
"Such programs are big business. Around €25 billion (£22 billion; $28 billion) in foreign direct investment has flowed into the EU through these schemes over the last 10 years," it said.
EU Justice Commissioner Vera Jourova said people obtaining an EU nationality "must have a genuine connection to the member state concerned".
"We want more transparency on how nationality is granted and more cooperation between member states. There should be no weak link in the EU, where people could shop around for the most lenient scheme."
The commission says it has several areas of concern: