A police spokeswoman told AFP an international warrant for Ivica Todoric, the prime suspect in an ongoing probe, will be issued once they officially receive the warrant from the prosecutors.
Along with 14 others, including his two sons and other former top executives at the company, Todoric is suspected of abuse of trust, forging official documents and failure to keep proper business records.
Todoric's lawyer Cedo Prodanovic said earlier his client was abroad and would "return when it will be needed".
Local media reported that Todoric was in Britain.
Twelve people were detained Monday in a series of raids in the Croatian capital including at Todoric's home, but neither he nor his sons were found.
One his sons, Ante Todoric, returned to Croatia and was questioned by the prosecutors Friday.
However, he declined to comment on his father's whereabouts.
With around 60,000 employees, two-thirds of whom are in Croatia, Agrokor is the largest employer in the Balkans.
The firm also has businesses in neighbouring Bosnia, Serbia and Slovenia.
According to an audit published last week, the debt-ridden food group made a loss of 11 billion kunas (1.5 billion euros/$1.8 billion) in 2016 and the value of its capital was cut by nearly three billion euros ($3.5 billion).
The food and retail group ran up its debt through aggressive expansion and expensive borrowing.
The government of the European Union member in April named a crisis manager to lead a restructuring process which would last up to 15 months.
If it was not successful within that time frame, bankruptcy proceedings would be initiated.
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