A Royal Gibraltar Police (RGP) spokesman said it received an "unofficial report" from the Guardia Civil on Wednesday about missiles being thrown at its officers from the motorcycle lane, as well as verbal abuse.
However, RGP were "unable to substantiate" accusations and continuing to investigate.
This has allegedly taken place at the peak of extensive queues to exit Gibraltar which at their height reached four hours.
The alleged missile throwing is reported to have come from the area of the motorcycle lane which at the time was full of cross-border workers unable to return home.
It came after insults and abusive comments were directed at the Guardia Civil.
The RGP is, notwithstanding the number of RGP officers present at the frontier managing the traffic, unable to substantiate the complaint at this time.
The matter is under investigation.