Six people suffered minor injuries in the crash on Thursday near the port city of Cartagena in Murcia region, authorities added.
The incident - which did not derail the train but briefly disrupted traffic on the line - came four days after a high-speed train collision in the southern Andalusia region killed at least 43 people.
Two days after that, a commuter train derailed after a containment wall fell on the track due to heavy rain near the city of Barcelona, killing the driver and seriously injuring four passengers.
The main train drivers' union called a country-wide strike over safety standards after that and a second collision in the northeastern Catalonia region on the same day.
On Thursday, "a street-lighting basket crane vehicle ... encroached on public railway land with its arm, striking the windows of a metric gauge train that was passing by at the time," Transport Minister Oscar Puente wrote in a post on X.
The injuries were minor, a spokesperson for the central government's representative in Murcia told Reuters.
Alcohol tests on both the train driver and the crane operator were negative, they added.
Firefighters on Thursday rescued Boro, a dog missing since Sunday's train accident, reuniting him with his owners in a rare moment of relief amid mourning for the victims of the high-speed train crash which also injured more than 120 people.
Boro, a cross between a schnauzer and a water dog, was riding on one of the trains with his owner Ana Garcia Aranda and her pregnant sister at the time of the crash.
Both women were injured, with the sister hospitalised in intensive care.
Relatives had pleaded with the public for help finding the dog.
"If I can't do anything for (my sister), at least I hope I can find Boro," Garcia Aranda said earlier this week in comments reported in Spanish media.
Police first spotted the dog near the crash site on Wednesday but he ran off when officers tried to approach him.
Firefighters caught him the following morning.
"We knew since yesterday the area where he could be, and today we were finally able to find him and bring him with us, so he can be returned to his family," one of the firefighters told reporters.
The dog has since been reunited with relatives.
"It has been very difficult and very beautiful," a family spokesperson said.
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