Sato Shuuhou (the author of "Say Hello to Black Jack") disclosed on his website the amount of payment for a manuscript and the royalties for the Tankobon. He said manga authors go into the red only with the payments for the publication in the magazines. When a manga series gets popular and its Tankobon is published, the author can make a profit from the royalty.

($1 = 100 yen)

Umizaru (1998)
Payment: 10,000 yen per page x 80 pages a month
= 800,000 yen a month
Personnel expenses for three assistants: 570,000 yen a month
Material expenses for manga drawings: 100,000 yen a month

Tokko no Shima (2006)
Payment: 25,000 yen per pages

Say Hello to Black Jack
Manuscript: 35,000 yen per page x 450 pages a year
= approx. 16 million yen a year
Personnel expenses for six assistants: 18 million yen a year

Royalty of Tankobon: approx. 50 yen per copy (8 -10% of one copy of Tankobon priced 500 - 600 yen)

It's extremely rare that a manga author makes public the specific numbers of the payments.

Sources: Sato's official website, Getnews