WASHINGTON — Most of the biggest challenges facing the Environmental Protection Agency — climate change, major new regulations on power plant emissions, biofuels production and enforcement of clean air and water laws — were virtually absent from Thursday’s confirmation hearing for President Obama’s nominee to head the agency, Gina McCarthy.

Instead, Republicans on the Senate Environment and Public Works Committee repeatedly returned to relatively arcane disputes over e-mail accounts used by top officials at the agency, whether the department had made public all the research data used in writing past regulations and whether it had pursued a litigation strategy that bypassed state environmental officials.

Ms. McCarthy, 58, is currently director of the agency’s Office of Air and Radiation and has had limited responsibilities in the areas singled out by Republicans on the committee. Unlike Mr. Obama’s recently departed E.P.A. administrator, Lisa P. Jackson, and several other predecessors, Ms. McCarthy did not have a second agency e-mail account under an alias or use a private e-mail account to help weed out the hundreds of thousands of unsolicited e-mails that pour in each year.

Republicans have been pursuing the use of secondary e-mail accounts and aliases at the agency since last year, calling it an effort by officials to evade federal open records laws. The E.P.A.’s inspector general has opened an inquiry into the matter.