We use density functional theory to study the effect of molecular adsorbates on the conductance of metallic carbon nanotubes (CNT). The five molecules considered (NO2, NH2, H, COOH, OH) lead to very similar scattering of the electrons. The adsorption of a single molecule suppresses one of the two available transport channels at the Fermi level while the other is left undisturbed. If more molecules are adsorbed on the same sublattice, the remaining open channel may or may not be blocked, depending on the relative position of the adsorbates. If the relative positions satisfy a simple geometric condition, this channel remains fully open independently of the number of adsorbed molecules.