The tournament is the last big event before the tennis tour moves to Roland Garros at the end of May but Nadal is still not in good enough shape to compete following the hip injury he suffered at the Australian Open.
Nadal had hoped to be fit by the start of the clay-court season but a gloomy update last month revealed the treatment he had been having had not worked.
The 36-year-old said on Twitter on Friday: "Hello everyone! I am very sorry to announce that I will not be able to be in Rome.
"You all know how much it hurts me to miss another one of the tournaments that have marked my professional and personal career for all the love and support of the Italian tifosi.
"Despite having noticed an improvement in recent days, there have been many months without having been able to train at a high level and the re-adaptation process has its time, and I have no choice but to accept it and continue working."
Nadal has won the title in Rome 10 times and has never gone into the French Open before without at least one warm-up event on clay.
For all his injury troubles, Nadal has never failed to play at Roland Garros since the first of his 14 titles in 2005, although he did pull out ahead of the third round in 2016 because of a wrist problem.
There are events in Lyon and Geneva the week before the start of the French Open on May 28 that Nadal could potentially seek wild card entry to but his hopes of a 15th title in Paris appear to be receding by the day.