Katherine Gallagher Robbins, a senior policy analyst with the National Women's Law Center, pointed out research showing that moms are often perceived—consciously or not—as less valuable workers. She noted a study in which participants were given two sets of résumés, with one set including activities that would point to being a parent.
The résumés that implied the woman was a mother generally got lower competency and commitment ratings and a lower recommended salary than those of a woman without children, while résumés suggesting a man was a dad commanded a higher salary than those for a man without kids.
Budig's research shows that the effect on earnings is true for all parents. Looking more narrowly at white women only, however, she found that the mommy penalty is especially strong for low-wage women. They are more likely to have trouble balancing less flexible jobs with the often-unexpected demands of parenthood, like a sick kid, she said.
"Women who earn less pay more—they pay a higher proportional penalty for kids," Budig said.
Her research also has shown that married white moms pay a higher penalty than single moms after accounting for other factors, like age and the demographics of who gets married. But white women who are in the highest earnings bracket do not seem to be subject to the penalty.
In addition, her research found that the fatherhood bonus is especially true for well-educated white and Hispanic men.
"Men who conform to expectations of what makes a good man—being a highly educated, married father—[are] more valued as an employee," Budig said.
The reports come as working mothers are increasingly important to family finances. A Pew Research Center report released earlier this year found that women are either the sole or primary breadwinner in 40 percent of U.S. households with children under age 18, in many cases because they are single mothers. That compares with just 11 percent in 1960.
"It really is an economic concern not just for women but for their families in general," said Robbins at the law center.
(Read more: How the weak jobs recovery slammed men and women)
Blau, the economist, noted that families are changing in other ways and that men are much more involved in children's lives than they were a generation ago. The shift in attitudes about home life could eventually lead to changing attitudes about parents' position in the workplace.
As a practical matter, she said, more women are pursuing the type of educational specialty that is valuable to employers, such as a law degree or an MBAs. That could spur companies to start thinking more about keeping these highly educated moms happy, loyal—and well compensated.
"It's sort of incumbent … upon employers to be concerned about these issues because they want to have the most productive workers," Blau said.
—By CNBC's Allison Linn. Follow her on Twitter @allisondlinn and Google or send her an email.