They were welcomed by gold-winning female discus thrower Sandra Perkovic and men's trap shooter Giovanni Cernogoraz, who had arrived in Croatia earlier.
The medalists were thanked by Sports Minister Zeljko Jovanovic, Zagreb Mayor Milan Bandic, and Croatian Olympic Committee chairman Zlatko Matesa.
"I have the privilege of being minister when you scored the biggest success in the history of Croatia's competition in the Olympics," said Jovanovic.
The medalists were later received by Prime Minister Zoran Milanovic in his office.
"Thanks for the excellent results, which are the best so far, but this doesn't matter. Not much would have changed had you come back with fewer medals. If you had won more, great! Sport is first and foremost a culture and a way of life," he said.
Milanovic said the government would keep its promise and introduce compensation for Olympic medalists which would be a little more than symbolic and would provide athletes with a decent future after they turned 45.
He said the government would continue to help the Olympic athletes as much as it could because they deserved it.
But, it is a time of crisis that will last for years, not only in Croatia, and the first to pull out of it will be those smartest, most enterprising and most persevering, said the prime minister. "That's true in sports and it's true in the economy as well."
Croatia's Olympic athletes and medalists were later welcomed by cheering crowds in Zagreb's central square.
The London Games were the most successful Olympics for Croatia, which won three golds, one silver and two bronzes, ranking 26th among the 85 countries that competed in the event.