The Foreign Office lodged a formal complaint with Spain after a British diplomatic bag was opened by a Spanish border guard.
Gibraltar's chief minister is to meet David Cameron amid allegations that Spanish border police have come under attack from angry motorists.
Pictures posted on Twitter show Spanish divers hanging flags over the controversial boulders.
The Spanish ships which entered British waters off Gibraltar acted in an "unlawful" and "dangerous" way, the Foreign Office has said.
"Not only were the actions of the survey vessel unlawful, but it was accompanied by a Spanish Guardia Civil vessel whose dangerous manoeuvring presented a significant safety concern on the waters," Europe minister David Lidington said.
The incursion by a Spanish ship into British waters off Gibraltar is "provocative", "unlawful" and "a violation of our sovereignty", the Europe minister David Lidington has said.
David Lidington was speaking after a Spanish state research trip entered British waters along with a vessel belonging to the Guardia Civil, the part of Spain's police force responsible for protecting the coastline.
According to the United Nations Convention on the Law of the Sea, the waters around Gibraltar are indisputably British territorial waters, under United Kingdom sovereignty, in which only the United Kingdom has the right to exercise jurisdiction.
Her Majesty's Government takes a grave view of any attempt by Spain to exert authority or control within British Gibraltar territorial waters and considers such incursions as a violation of our sovereignty.
I strongly condemn this provocative incursion and urge the Spanish government to ensure that it is not repeated.
The Foreign Office has summoned the Spanish ambassador after a "serious Gibraltar incursion", Reuters reports.
Gibraltar's Chief Minister has expressed his pride at the draw for Euro 2016 after the British overseas territory was forced to switch groups following its brief pairing with Spain.
The blind draw in Nice, France saw the territory, which will compete in qualifying for the very first time, briefly drawn in the same group with Spain before they were moved for "political reasons".
Fabian Picardo, tweeted:
Exciting day. Exciting draw. Proud of GFA's involvement in Euro16. Love the group we are in. Can't wait for the games. All of them!
Gibraltar will now face Scotland, the Republic of Ireland, Germany, Poland and Georgia in Group D when fixtures begin in September.
For the latest football news visit ITV Sport
Gibraltar has been moved after it was selected to be in a group with Spain during the Euro 2016 football tournament draw.
The blind draw in Nice, France, briefly saw the British overseas territory paired up with the current European and world champions in Group C.
But European football's governing body UEFA had already announced in December that Gibraltar and Spain would be kept apart amid continuing political tensions over the territory's sovereignty.
Gibraltar was switched to Group D, where they will face Scotland and the Republic of Ireland among others.
See more on the draw from ITV Sport
A Spanish warship caused a training exercise by British forces to be suspended after entering the waters around Gibraltar.
The Gibraltar Squadron's patrol boat HMS Sabre shadowed the ship, which is said to have used a fake name and call sign, the Gibraltar Chronicle reports.
Royal Navy special forces personnel are believed to have been carrying out a parachute jump at the time, the newspaper said.
Warnings were made to the vessel, which only left the area after radioing back that it was in Spanish waters.
In November, the Foreign Office condemned an incident in which a British diplomatic bag was opened and searched by Spanish Guardia Civil officers on Gibraltar's border with Spain.
The packages that were opened on Gibraltar's border with Spain were not diplomatic bags, Spain's Foreign Minister said.
Jose Garcia-Margallo reportedly told the BBC: "There is no incident. If it is not a diplomatic bag, there is no diplomatic incident. A bag was opened, which was not a diplomatic bag."
A Foreign Office spokesman said the bags were "clearly marked as the property of HM Government" and, as such, were covered by the Vienna Convention.
British warships should be sent to Gibraltar to show the UK's determination to defend the region, Conservative MPs urged today.
Already tense relations between Spain and the UK were heightened earlier this week after a diplomatic bag was opened by a Spanish border guard on the border.
Peter Bone said Royal Navy ships should make a "goodwill visit" to the territory to build trust with the Gibraltarians, before adding he would prefer to send a couple of gunboats instead.
Fellow Tory and former minister Bob Neill went on to ask the Government to consider reinforcing the UK's naval deployments available in Gibraltar.
Former army colonel and now Tory MP Bob Stewart suggested last week that Britain should send major combat units to train in Gibraltar to show its determination to defend the region.
Spain has given an assurance there will be no repeat of the incident in which officials on the border with Gibraltar searched a British diplomatic bag, the Foreign Office has said.
The incident, which took place on Friday, was described by a Foreign Office spokesman as a "serious infringement" of international diplomatic protocols.
– David Lidington, Minister for Europe
In our protests we requested an urgent explanation of this incident from the Spanish Government and sought assurances that there will be no further interference with the UK’s official correspondence.
We have now received that explanation from the Spanish and have been assured that we will not see a repeat of these actions.