"A district court in Baku ordered Afghan Mukhtarli to spend three months in pre-trial detention," his lawyer Elchin Sadykhov told AFP.
"My client was charged with illegal crossing of the border, money smuggling, and resisting police," Sadykhov said, adding that Mukhtarli may face up to seven years in jail if found guilty.
Mukhtarli, 43, has lived in self-imposed exile in Georgia since 2015 after investigating Azerbaijan's strongman leader Ilham Aliyev for corruption. He was reported missing by his wife on Tuesday.
He was then taken to Azerbaijan and charged with smuggling 10,000 euros ($11,200), Sadykhov said, adding that the banknotes had been planted in his pocket.
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Prosecutors in Azerbaijan said that Mukhtarli was detained by border guards after trying to "illegally cross" the country's border and that the money was found during a subsequent search.
Georgian President Giorgi Margvelashvili said in a statement that Mukhtarli's "disappearance from the Georgian territory" was a "serious challenge to the Georgian state and its sovereignty".
Georgia's interior ministry said in a statement that it had opened an investigation into what it called an "illegal detention".
Rights groups denounced Mukhtarli's suspected abduction, and warned that he could be at risk of torture.
"He is a prisoner of conscience detained solely for his work as a journalist," Levan Asatiani of Amnesty International told AFP.
Asatiani said it appeared that the authorities in pro- Western Georgia "were complicit in the harrowing cross-border abduction".
"Azerbaijan should immediately free him," he said in a statement.
The authorities in oil-rich Azerbaijan have faced strong international criticism over claims they routinely harass and jail the president's opponents, though the government has denied the allegations.
Aliyev, 55, took over in 2003 after the death of his father Heydar Aliyev, a former KGB officer and communist-era leader who had ruled Azerbaijan with an iron fist since 1993.
Georgia has long been an asylum destination for Azerbaijani dissidents fleeing persecution at home. It has faced mounting pressure from Baku over sheltering Aliyev's critics.