"We as a family are extremely disappointed by the outcome of 12 years," he said.
"We would have expected a sentence of at least 20 for the brutal, premeditated murder of our father.
"For the verdict to be a sentence of only 12 years is unjust not only for us as a family, but Indonesia in general."
The prosecutor said he was considering an appeal.
The body of Mr Ellis was found wrapped in plastic in a rice field last October.
The popular expat, who had made his wealth in telecommunications, aviation and property, had been set upon in his own villa, held down on the kitchen floor and his throat slashed with a knife.
His wife had been sitting in the next room. She helped dispose of the body and ordered her two maids to clean the bloody kitchen.
She initially reported Mr Ellis missing and lied to her sons about their father's whereabouts.
When she did confess to orchestrating the crime, she claimed she was desperate after years of neglect and being denied a divorce.
The Ellis family claims she was not neglected, and that her manipulation extended to submitting to the court a false statement purportedly signed by John Ellis, asking for a lenient sentence.
"We are very upset about the accusations against our father which Noor has fabricated in order to defend herself," Peter Ellis said outside court.
"We are also still in disbelief over the falsified statement, which is now being used as evidence to support Noor, and would have thought such forgery was both a crime in itself and further evidence of guilt of Noor and other accomplices."
Ellis' story changed a number of times after her arrest.
She first claimed she only wanted to teach her husband a lesson, and was shocked to find the five men she paid $14,000 had killed him.
Later, she admitted she had ordered Mr Ellis killed, but "not sadistically" - a deal she had sealed with a pinky swear.
Judge Wirakanta said he accepted Ellis ordered the murder because she felt hurt.
She had enough time to change her mind, but didn't, he said.
"It's true the defendant and the victim have not lived harmoniously for about 11 years and the defendant wasn't given adequate mental and physical care," he said.
Two of the five men involved, known as Urbanus and Yohannes, were also sentenced to 12 years' jail on Wednesday.
The others as well as two maids are expected to be sentenced soon for their roles.
Mr Ellis has been laid to rest in New Zealand.
-AAP
