The effect of interfibrillar interaction on the charge transport of doped polyacetylene is investigated by studying the high field magnetoconductivity of iodine doped helical polyacetylene. The zero-field resistivity ratio, ρr = ρ(1.2 K)/ρ(300 K), is comparable to that of stretch-oriented high-density polyacetylene, which indicates the partial alignment of chains inside a polymer fiber. At low magnetic fields, the small negative component of magnetoconductivity was observed and its magnitude increases as the ρr value increases. In the high field region, the magnetoconductivity is positive and it clearly shows the linear dependence on the magnetic field up to H=30 T. The linear field dependence of magnetoconductivity is different from what is expected in the three-dimensional weak localization picture. For the same ρr value samples, the magnitude of negative magnetoconductivity of S-polyacetylene is much bigger than that of R-polyacetylene, which could be attributed to the difference in the degree of helicity determining the strength of interfibrillar interaction.