In the context of the article cited (and indeed generally in Spain), "centro superior" simply means a university or equivalent body. The most common and usual generic term for this is "institution of higher education" or "higher education institution". "Centre/center" and "institute" are terms that refer to a smaller and more specialised body, normally devoted to one particular branch of study, and often a specific research entity within a university. However, "centro" does not mean that here. In Spain, a "centro" is an educational institution or establishment; it can refer to a school or to a university or college, but "superior" can only be the latter.

In the United States, the term "Higher Learning" is fairly commonly used, though much less so in the United Kingdom and Ireland. However, "higher education" is valid in all English-speaking areas. Here, just to take one example, is the Texas Education Code, where "Institution of higher education" is used as the relevant generic term:
http://www.statutes.legis.state.tx.us/Docs/ED/htm/ED.54.htm

The article is obviously referring to research funds, but it is not talking about non-teaching research institutes. On the contrary, it is universities as teaching and research bodies; it refers to the Bologna process and "preparar a sus alumnos para el mercado". So it is about higher education, not just research (the former, in any case, intrinsically involves the latter).

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Note added at 1 hr (2012-01-02 21:51:03 GMT)
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Further evidence that "centro superior" simply means "universidad" in this context is that the subheading of the article reads "Los centros superiores captan un 9% de sus fondos de entidades privadas", and in the body of the article, this is expressed as: "El 9% de la investigación universitaria (317 millones) se financia desde las empresas". Therefore the "centros superiores" here are not research centres in universities, but universities themselves: it is referring to the totality of the research carried out within a university. Even nowadays, outside the experimental sciences, a large proportion of university research is not carried out in research centres, but individually or in small teams within teaching departments.

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Note added at 1 hr (2012-01-02 22:22:14 GMT)
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This use of "centro superior" as "centro de enseñanza superior" is standard. Here are further examples:

"Los centros superiores recibirán 3,5 millones para intercambios Erasmus
Un total de 13 centros de enseñanza superior y 1.051 alumnos serán beneficiarios
Las universidades e instituciones de enseñanza superior andaluzas recibirán 3,5 millones de euros para el desarrollo del programa de intercambio Erasmus en concepto de subvención para un total de 1.051 alumnos con escasos recursos económicos"
http://www.diariodecadiz.es/article/andalucia/313788/los/cen...

"La falta de competitividad de los centros superiores
Ninguna universidad española está entre las 100 mejores del mundo"
http://www.elpais.com/articulo/sociedad/educacion/suspende/e...

Of course, there are also "centros superiores no universitarios", such as music, dance and film schools, but this article is not referring to them.

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Note added at 1 hr (2012-01-02 22:23:13 GMT)
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"Research centres/centers" are normally called "centros de investigación" or "institutos de investigación".