The Barcelona-based bank said the restructuring was needed following the purchase of smaller rivals Banca Cívica and Banco de Valencia which has caused its staffing levels to soar.
"In order to adapt to the current environment and improve the efficiency of resources, and following the recent integration of the savings group formed by Banca Cívica and the forthcoming incorporation of Banco de Valencia, CaixaBank considers it necessary to carry out a restructuring plan," it said.
"The implementation of this restructuring will affect some 3,000 employees," the bank added in a statement, adding it would negotiate the exact amount of layoffs with unions.
CaixaBank bought Banca Cívica and rescued lender Banco de Valencia last year, although the latter has not yet been fully integrated.
It had 32,625 employees at the end of 2012, compared with nearly 27,000 a year earlier, while its network grew by over 1,000 branches.
Caixabank's net profit plunged 78.2 percent to €230 million ($312 million) in 2012 over the previous year as a result of having to make greater provisions to cover potential real-estate losses.
Spain's real estate market crashed in 2008, leaving lenders awash with bad loans and prompting a wave of consolidation and hefty job losses in the sector.
Last month Spanish bank workers staged nationwide protests over the thousands of layoffs in the industry and against the top executives they hold responsible.
Spain's banking sector shed over 28,000 jobs from 2008 to 2011, according to the Bank of Spain.
Banks employed 243,041 people in 2011, the last year figures are available, down from 270,855 in 2008. Meanwhile, the number of branches had dropped to 39,843 in 2011 from 45,662 in 2008.
Unions predict the bank sector will shed 20,000 more jobs over the next five years.
Earlier this month bailed-out bank Bankia announced it would slash 4,500 jobs.
Prime Minister Mariano Rajoy last year secured an agreement for a European Union rescue loan of up to €100 billion ($130 billion) to fix the banks's balance sheets, and a first slice of €37 billion has already been pumped into stricken banks.
CaixaBank was born July 1, 2011, when Caixa savings bank group listed its retail banking activities.
Banca Civica also made its debut in July 2011 after it was formed from the merger in 2010 of the regional savings banks Caja Navarra, Cajasol, Caja de Burgos and CajaCanarias.