The number of people registered as unemployed rose by 25,572 people from the previous month to 4.72 million, the first increase since February, the Labour Ministry said.
The jobs landscape looked brighter, however, when the figures were corrected to smooth out seasonal variations, showing the jobless claimants total fell by 35,631 people to 4.83 million.
This was the best seasonally adjusted result for September on record, said Spain's Minister for Employment and Social Security Fátima Báñez.
The government and financial markets, however, usually focus on the raw figures rather than the seasonally adjusted data.
Spain's state secretary for employment, Engracia Hidalgo, said government reforms, which make it cheaper to lay off workers and easier to change work conditions, would improve the labour market.
"There is still a lot of work ahead to turn the situation around but we are convinced that the adopted reforms are the way to recovery and as such the necessary means for our country to recover the path of growth and sustained creation of stable, quality employment," she said in a statement.
Only 7.69 percent of job contracts signed in Spain in September were for ongoing positions, with just over 50 percent being full-time roles.
Spain, the euro zone's fourth-largest economy, is still struggling to overcome the aftermath of a decade-long property bubble that imploded in 2008, destroying millions of jobs and sending debt levels soaring.
The government has said it expects the economy to emerge from a two-year recession in the third quarter.
The official unemployment rate, which is calculated on a broad household survey released every three months, hit 26.26 percent in the second quarter of this year.
Last week, Prime Minister Mariano Rajoy's conservative government forecast that the unemployment rate would be 26.6 percent in 2013 and 25.9 percent in 2014.
The government raised its outlook for economic growth next year to 0.7 percent from an earlier forecast of 0.5 percent.
The International Monetary Fund has warned that Spain faces five more years with an unemployment rate topping 25 percent unless it enacts new reforms including measures to help firms slash wages instead of axing staff.
Spain has two sets of unemployment figures, providing different estimates.
Employment Ministry figures, such as those released on Wednesday, are based on the number of unemployed persons registered in their offices.
Spain's stats office, the INE, however, conducts a survey (the EPA) of 65,000 Spanish households to obtain its results.
The EPA includes responses from some people who want to work but who are not registered in the employment offices.
The responses also include those who fall into other special working categories which are not recorded by the Ministry.
This explains why EPA unemployment figures are higher than those of Spain's Employment Ministry.