Judge Santiago Torres has charged the pair, along with 12 others, with offences relating to destruction, suppression or concealment of public documents and using false documents, the Madrid court said in a statement.
The accused have been called to appear in court on May 20 and 21 to answer the charges and the judge also ordered an examination of the veracity of the club accounts presented at the assembly, it added.
A Real Madrid spokeswoman said the club had no immediate comment on the court announcement. Any statement would be published on their website, she added.
Calderon's resignation in January threw the Primera Liga club into institutional turmoil and the June 14 elections have paved the way for a possible comeback by former president Florentino Perez.
Calderon, who replaced Perez in 2006, was accused of manipulating voting at the assembly, which was later declared null and void. He has denied any wrongdoing.
Real, Primera Liga champions for the past two seasons, look set to lose their crown to Barcelona, who are seven points clear at the top of the table with four matches left and who inflicted a record 6-2 defeat on second-placed Real in Madrid on Saturday.
Perez has yet to officially confirm he is standing for president but he is due to give a news conference on May 14 to outline his plans.
Spanish media have linked his candidacy with moves for Cristiano Ronaldo, Kaka, Cesc Fabregas and Xabi Alonso among other players.
