The chase started 18 kilometres (11 miles) into the Strait of Gibraltar but ended at around 3:00 am (0100 GMT) on the shoreline in Sandy Bay, a beach on Gibraltar's east side overlooked by residential homes.
The smugglers jettisoned bales of drugs before hitting a submerged reef and abandoning their beached vessel with Spain's customs service in hot pursuit.
According to the Royal Gibraltar Police and eyewitness accounts, the Spanish helicopter hovered low over the beached speedboat while the patrol boat deployed a small dinghy, which entered the sheltered lagoon in Sandy Bay and headed to the shore.
Gibraltar police were deployed to the scene and arrested two of the suspected smugglers on land. A third man managed to escape.
Authorities in Gibraltar said Spanish customs had failed to alert them about the chase or request assistance.
"We consider this has been a serious and unnecessary failure on the part of the Spanish customs service which has had outrageous consequence in respect of the violation of our sovereignty," said Gibraltar's Chief Minister, Fabian Picardo, in a statement.
After the events of the last 48hrs, here is our statement and a photograph of the RHIB confiscated. pic.twitter.com/diKQ5MH9hc— Fabian Picardo (@FabianPicardo) August 9, 2015
He blamed Spanish customs for acting a way "that, in effect, has allowed a criminal who should be behind bars to get away."
Foreign Office Minister Hugo Swire, in a statement, condemned the "incursions" as "unlawful."
"These repeated incursions into British Gibraltar Territorial Waters are a clear violation of UK Sovereignty by another EU country and we will be raising this as a matter of urgency with the Spanish authorities," he said.
This is the most serious in a string of similar incidents in the waters around Gibraltar, which are claimed by both Britain and Spain.
Although police and customs in Gibraltar regularly cooperate with their Spanish counterparts, disagreements over jurisdiction mean there is no formal protocol in place.
As a result tense exchanges are commonplace, particularly when Spanish vessels attempt to take action in waters that the UK regards as British but which are also claimed by Spain.
Earlier this month a Spanish customs vessel chased a speedboat into a demarcated swimming area off another Gibraltar beach.
The action was dubbed as "irresponsible" by Gibraltar and led the British government to lodge a diplomatic protest with officials in Madrid.
Smuggling of hashish from Morocco through the strait of Gibraltar reaches a peak in the summer when the weather is fair.
Spain is one of Europe's main entry point of drugs coming from Africa or South America.
Spain ceded Gibraltar to Britain in perpetuity in 1713 but has long argued that it should be returned to Spanish sovereignty. London says it will not do so against the wishes of Gibraltarians, who are staunchly pro-British.