Social Security and Labor Minister Linas Kukuraitis confirmed the decision on Wednesday.
"I am happy with today's decision, because the two kids will reunite with their dad in their home," Kukuraitis said in a press release.
"At the same time, I hope that the manager of the case and his team, as well as other municipal experts in Kaunas, will provide all the necessary assistance to the children and their dad and mom," he said. "I am calling on the dad and mom to accept that assistance."
The minister said he sincerely believed that the couple love their children and called on the parents, child rights protection specialists, municipal officials and the general public "to join forces".
The family told the media that their children had been taken away based on a report from a passerby saying that he saw the mother smacking her son on the arm as he tried to run into the street.
Law-enforcement officials are conducting a pre-trial investigation into the circumstances.
Meanwhile, children's rights specialists say the two young children were separated from their family due to safety concerns after the parents refused to cooperate with police officers and child protection officials, but admit that mistakes were made in responding to the situation.
According to the State Child Rights Protection and Adoption Service, there were 513 cases of children placed into temporary foster care between July 1 and October 22 this year, compared with 710 between July and December 2017.
Some 6,000 reports about children being in danger have been received since amendments to Law on the Fundamentals of Protection of the Rights of the Child came into force on July 1 this year. Sixty-four percent of these reports have proved to be unfounded.
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