The filing cites sexual discrimination and harassment, wrongful termination and retaliation, among other complaints.
Fuqua denies all the charges against him and believes he will be completely vindicated in court.
J. Edward Hollington, an Albuquerque attorney who represents the two women, Julie Baird and Julie Rasor, said the case will head into the discovery phase in the next three to four weeks.
"While in the early stages, we expect to take up discovery matters of depositions and the pre-trial process before the end of April," Hollington said when reached by phone.
The complaint covers more than two years of alleged inappropriate or abusive behavior by Fuqua toward women employees. Fuqua allegedly inappropriately touched and threatened the women, according to the complaint.
Also cited are alleged sexist comments and Fuqua-approved $5,000 raises for male department heads only.
"There is quite a lot I've been accused of, but not one bit of proof," Fuqua said. "I can promise you, it's not going to end the way some people think it is. I have full confidence in our attorneys and the judge who will preside over the case."
City manager since 2010, Fuqua said he has faults like anybody else, but being a sexual harasser is not one of them.
"That's not me," said Fuqua. "I've been happily married 33 years."
James Fenton can be reached at firstname.lastname@example.org; 564-4621. Follow him on Twitter @fentondt.