The decision follows the state's widely condemned execution last year in which guards failed to connect a back-up intravenous line to Stanley "Tookie" Williams, the former Crips gang leader who later wrote a number of anti-gang books.
Earlier this week, Florida executioners failed to insert needles correctly into condemned killer Angel Diaz, which meant lethal chemicals did not go directly into his veins, according to the state's medical examiner.
Florida's incoming governor, Charlie Crist, responded by saying he would halt executions until a commission investigated the state's procedures.
Cruel and unusual
Death penalty opponents have for years argued that lethal injection is cruel and unusual punishment barred by the US constitution, but only such recent instances have given legal and political traction to their arguments.
"When properly administered, lethal injection results in a death that is far kinder than that suffered by the victims of capital crimes," said Fogel, who earlier this year visited the death chamber at San Quentin state prison north of San Francisco.
"When properly administered, lethal injection results in a death that is far kinder than that suffered by the victims of capital crimes"
California federal judge
"At the present time, however, defendants' implementation of California's lethal-injection protocol lacks both reliability and transparency.
"In light of the substantial questions raised by the records of previous executions, defendants' actions and failures to act have resulted in an undue and unnecessary risk of an eighth amendment violation. This is intolerable under the constitution."
Lethal injection is used in 37 US states, but legal challenges have delayed such executions this year in not only California and Florida, the first and fourth most populous states, but several others including New Jersey and Ohio.
The US has executed 53 people in 2006, a 10-year low, according to the Death Penalty Information Centre.
California has long punished convicted criminals with execution. Its San Quentin prison hanged the condemned from 1893 and turned to lethal gas in 1938. It began using lethal injection in 1994 after a federal judge found gassing cruel and unusual.
Florida legislators voted to switch to lethal injection in 2000 after a series of bungled executions using the state's electric chair, including one where flames shot from a prisoner's head.
|Fogel has ruled that the use of lethal injection|
is unconstitutional in California
Executioners now typically attach two intravenous lines to condemned US inmates, one tube acting as a backup to assure a continuous flow of the three chemicals that anaesthetise, paralyse and then kill.
In the Williams execution, prison guards struggled for 25 minutes to insert the intravenous lines and it took another 10 minutes for the lethal drugs to take effect, said Barbara Becnel, a witness to the execution and co-author of Williams' anti-gang books.
Journalists at several recent California executions have seen guards struggle to insert the IV lines to the condemned killer.
Witnesses in Florida this week said Diaz appeared to grimace and gasp for breath in what was supposed to be a quick but painless procedure. Prison officials had to give Diaz the drugs twice and it took him 34 minutes to die from the start of the execution.
Richard Steinken, a Chicago lawyer who has worked with condemned inmate Michael Morales, whose case sparked Fogel's decision on Friday, said: "The court, I think correctly, recognised that there are severe flaws in the system.
"Whether it can be fixed remains to be seen."