Speaking in Brussels, Frattini's spokesman Friso Roscam Abbing said six EU countries have either joined the project or will do so shortly.
Abbing said the pilot project has been set up within the Hungarian embassy in Moldova with Austria, Slovenia, and Latvia already taking part.
He said those four countries will be joined in the future by Denmark and Estonia.
Hungary is the only one among the six countries with an embassy in Chisinau.
Abbing said administrators from each country will pool together their skills, technical equipment, and knowledge in order to cooperate on the processing of visa applications from Moldovan citizens.
Each of the six countries will continue to issue their visas separately.
Among the countries operating the new visa center, Austria and Denmark are the only signatories of the Schengen Agreement.
The Schengen accord, which abolishes border checkpoints between member countries, currently covers 13 EU states, as well as EU non-members Iceland and Norway.
(RFE/RL's Romania/Moldova service contributed to this report)
Some visa fees are waived for certain applicants, notably for officials, students, athletes, scientists, or people receiving medical treatment.
From January 1, 2007, the price of a Schengen-zone visa goes up by nearly 75 percent from 35 euros to 60 euros. Twenty-six countries are signatories to the Schegen agreement. They include all the EU states, with the exception of Ireland and the United Kingdom, and include the non-EU states of Iceland, Norway, and Switzerland. However, only 15 of the signatories have so far implemented the system. The new EU members from Central and Eastern Europe are among those countries yet to implement the agreement. EU officials have said the price rise is due to the need to integrate biometrics identifiers, for instance fingerprints, into the visa-application process.
Under readmission treaties, EU member states can ask a country to readmit illegal immigrants. That applies to a country's nationals or any third-country nationals who have transited through its territory.