The Typhoon fighter planes were responding to an emergency signal emitted in error by a small civilian helicopter, which indicated it could have been hijacked or 'gone rogue', said an MoD spokesman.
But the fighter planes had been authorised to go supersonic and were already on their way to the helicopter. when its pilot realised the mistake, he added.
During the incident one of Royal Airforce Typhoon's emitted a sonic boom that shook houses in Coventry, Rugby and Leamington.
The MoD spokesman said: "We can confirm that a small civilian aircraft was transmitting inadvertently on an emergency frequency at approximately 18.10.
"Two typhoons from the Quick Reaction Alert (QRA) responded accordingly and authorisation was given from them to go supersonic, which resulted in the sonic boom.
"There was no actual threat to the civilian aircraft and they soon rectified their mistake."
Police and fire services in the West Midlands were inundated with phone calls about the noise shortly after 6pm from concerned members of the public in Bath, Swindon, Coventry, Rugby and Oxford.
Many people on Twitter and other social networking sites confirmed they had also heard the noise, some as far as Swindon and Oxfordshire.
A sonic boom is the sound associated with the shockwaves created when an object travels through the air and breaks the sound barrier. The noise contains large amounts of sound energy, meaning sonic booms are often mistaken for explosions.
It is the second time this year that a sonic boom has been created by a Typhoon aircraft. In January, the MoD confirmed that a loud noise heard by people across the north of England was caused by an RAF fighter jet breaking the sound barrier.
