"This is big stuff, and I'm really proud of these guys."
The chromosomes are numbered 5, 16 and 19. They are among 24 distinct bundles of DNA within our cells that contain the "code of life".
At the end of last year, the publicly-funded effort decoded chromosome 22, and a "working draft" of the entire set of chromosomes is promised by June.
Gene-rich areas
"Three chapters in the reference book of human life are nearly complete," said US Energy Secretary Bill Richardson, whose department has provided a large slice of the funding.
"This is big stuff, and I'm really proud of these guys."
The Joint Genome Institute researchers say they have mapped about 90% of the three chromosomes. The gaps, which will be filled in eventually, contain areas thought not to contain very important information.
Those areas that have been sequenced have an estimated 10,000 to 15,000 genes and comprise about 11% of a human's total genetic material. The researchers still have to order the code precisely and mark out the exact positions of the genes, the templates for the protein molecules that guide the form and function of cells.
Some of the genes on the newly mapped chromosomes contain defects that may predispose patients to certain forms of kidney disease, prostate and colorectal cancer, leukaemia, high blood pressure, diabetes and the damage to arteries known as atherosclerosis.
Public-private battle
The news is just the latest in a series of announcements to come from the private and public sector initiatives involved in decoding the human genome. Each side has disputed the quality and progress of the work undertaken by the other side.
Last week, private firm Celera Genomics said it had finished sequencing all the DNA (on all the chromosomes) in one person and was now putting the information into the right order.
Celera, which uses a different decoding technique to the public effort, only began its sequencing last year and plans to sell analysis of the human genome to drug companies when its work is completed.
Last month, Celera published the genome of the fruit fly (Drosophila melanogaster), the largest animal so far to have its genetic material fully sequenced. The research was a collaborative effort with public institutions.