The Foreign Office is lodging a formal complaint with Spain over the latest "unacceptable" delays at the border with Gibraltar.
The Royal Gibraltar Police said earlier that queues to enter Gibraltar had been around three hours, although there were no delays leaving.
"The Foreign and Commonwealth Office will be protesting to the Ministry of Foreign Affairs about the unacceptable delays seen this morning at the Spanish border with Gibraltar," a Foreign Office spokesman said.
Officials are still considering whether to mount a legal challenge to Spain over its imposition of additional border controls in the latest diplomatic spat between the two countries over the Rock.
Legal challenges could be mounted to heal the Gibraltar dispute
The Spanish action followed the construction by the Gibraltar authorities of an artificial reef which Madrid claims is designed to ruin fishing in the area.
Downing Street has described the controls as "politically motivated and disproportionate" - putting Spain at odds with EU laws on the freedom of movement.
The European Commission plans to send a team of investigators to the Gibraltar border in the next couple of weeks to observe the new controls, following complaints from several MEPs and EU citizens about the long delays.
Ignacio Ibanez, the director general for foreign affairs at Spain's foreign ministry, dismissed the threat of legal action, insisting the controls were imposed in response to an upsurge in smuggling of tobacco and other items.
"Gibraltar is not part of the EU customs area, also it is not (in the) Schengen area, so the obligation of the Spanish authorities is to control the border," he told Channel 4 News.
"We have been noticing in the last months and weeks a big increase in smuggling so we need to control this place and we are doing so."
He insisted that Spain would eventually succeed in its claim to recover Gibraltar from Britain.
"We are confident that in the end that we will have Gibraltar as part of Spain," he said.