Masipa, who acquitted the double-amputee Olympic athlete of murder during a trial in Pretoria in September, sentenced him to five years in jail. But under South African regulations, he can be released after 10 months.
Applying for an appeal of the case, Nel said 10 months was the shortest reasonable jail term Masipa could have provided, and he questioned what kind of term would be appropriate for less serious cases of reckless killing.
"This must be at the top end of negligence. What will happen to less negligent cases?" he said. "The precedent set by this court is shockingly low, that someone who acted with that degree of culpability should be sentenced to five years."
Masipa is expected to rule on the matter Wednesday.
On Valentine's Day 2013, Pistorius fired four shots into a toilet cubicle off his bathroom, killing his girlfriend, Reeva Steenkamp. He testified he heard a noise in the toilet that convinced him an intruder was coming out and that his life was in danger. Masipa accepted his story.
"An innocent woman was shot and killed in most horrendous circumstances, caused by gross negligence of this respondent," Nel said Tuesday, referring to Pistorius.
"The respondent knew there was someone in the toilet. He knew that. He deliberately fired four shots through the door. He knew ... that person would not be able to maneuver or escape. It's not someone who fired blindly. We're not dealing with a person who just grabbed the gun and fired. We're dealing with a trained person," Nel told the judge.
He said her judgment had shown excessive mercy at the expense of looking at the consequences of Pistorius' actions, and he argued that the athlete wasn't really remorseful.
In order to succeed in gaining leave to appeal, Nel doesn't have to convince Masipa of the need for a tougher sentence. He has to convince her there is a possibility that an appeals court would hand down a harsher penalty.
The prosecution is not only seeking to appeal the sentence, but Pistorius' acquittal on a murder charge as well. Nel told the court it was not a step he took lightly.
Much of the hearing involved technical points of law, revolving around the legal circumstances in which appeals by prosecutors are allowed.
Barry Roux, appearing for Pistorius, said the prosecutor was required to prove that Masipa had made an error in law, and that Nel had failed to do so.
"Every single point the state has made we have shown that the court has taken it into consideration before judgment. The state is not happy with the factual findings of the court and that is something it has no right to appeal to a higher court. The state has to show where the court went wrong in applying the law; it hasn't done that," Roux said.