We present V and I photometry for a sample of 220 globular cluster candidates in the Virgo galaxy M87. The sample is essentially complete to V=26. We confirm the bimodal colour distribution found by Elson & Santiago (Paper I), and find peaks at (V-I)=0.92 and 1.23. A comparison with the colour distribution of globular clusters in the Milky Way shows that M87 contains a large population of red clusters that is virtually absent in our Galaxy. We also confirm the suggestion in Paper I that the luminosity functions of the red and blue clusters are different. The brighter clusters are predominantly blue, while the fainter clusters are roughly equally divided between red and blue. The presence of two distinct subpopulations with different mean luminosities casts doubt on the common assumption of a universal luminosity function for globular clusters.