The founding session took place in Belgrade three months ago.
The Zagreb meeting focused on the issue of providing information to ethnic minorities in their mother tongue, minorities' participation in local assemblies, parliaments and other institutions, education in one's mother tongue and the financing of minorities' umbrella organisations.
Croatia's Assistant Foreign Minister Slavko Leban told reporters that today's session was constructive and open.
"We discussed all issues from the field of protection of ethnic minorities and the tone of the discussion and recommendations gives us reason to be optimistic," Leban told a news conference.
Serbia-Montenegro's Assistant Minister for Human and Minority Rights, Jelena Markovic, added that the committee wanted to solve a large number of problems as quickly and efficiently as possible.
According to her, both the Croatian minority in Serbia-Montenegro and the Serb minority in Croatia were dissatisfied with the provision of information in their mother tongue, particularly in the electronic media. This is one of the crucial issues addressed by the committee, she added.
Leban said that it was important that minorities could have TV broadcasts in their own languages.
In this context, the committee agreed to set up a Croatian editorial board in the Novi Sad TV station (northern Serbian province of Vojvodina) until the end of next month.
The two minority communities also believe that they should have more representatives in the local judiciary and police.