Venezuelan President Hugo Chavez has recalled his ambassador to Buenos Aires following a complaint by Argentina's leader, Argentine media report.
The blast was the worst terror attack in Argentina's history
President Nestor Kirchner is said to have contacted Mr Chavez over the conduct of ambassador Roger Capella.
Mr Capella is accused of supporting former Housing Secretary Luis D'Elia.
Mr D'Elia was fired for criticising an international arrest warrant for eight Iranian former cabinet ministers issued by Argentine prosecutors.
The warrants were issued over the ex-ministers' alleged involvement in a bomb attack on a Jewish cultural centre in Buenos Aires in 1994, in which 85 people were killed.
Correspondents say this is the latest in string of diplomatic incidents involving the Venezuelan ambassador.
The then Iranian authorities have been accused of directing Lebanese militia group Hezbollah to carry out the attack.
Iran has rejected the charges, describing it as a "Zionist plot".
Hezbollah has also denied its involvement in the attack.
The blast reduced the seven-storey Jewish-Argentine Mutual Association community centre to rubble.
Argentina's Jewish community has long called for answers to the crime
No-one has ever been convicted of the attack, but the current government has said it is determined to secure justice.
Over the years, the case has been marked by rumours of cover-ups and accusations of incompetence, but little in the way of hard evidence.
Minor figures have been named, including a policeman who sold the van used in the attack, but no-one has been convicted.
Local Jewish groups have long said the bombing bore the hallmarks of Iranian-backed Islamic militants.
The 1992 bombing of the Israeli embassy in Buenos Aires, which killed 29 people, also remains unsolved.