  We consider the 3D incompressible hypodissipative Navier-Stokes equations,
when the dissipation is given as a fractional Laplacian $(-\Delta )^s$ for
$s\in (\frac34,1)$, and we provide a new bootstrapping scheme that makes it
possible to analyse weak solutions locally in space-time. This includes several
homogeneous Kato-Ponce type commutator estimates which we localize in space,
and which seems applicable to other parabolic systems with fractional
dissipation. We also provide a new estimate on the pressure, $\|(-\Delta)^s p
\|_{\mathcal{H}^1}\lesssim \| (-\Delta )^{\frac s2} u \|^2_{L^2}$. We apply our
main result to prove that any suitable weak solution $u$ satisfies $\nabla^n u
\in L^{p,\infty }_{\mathrm{loc}}(\mathbb{R}^3\times(0,\infty))$ for
$p=\frac{2(3s-1)}{n+2s-1}$, $n=1,2$. As a corollary of our local regularity
theorem, we improve the partial regularity result of Tang-Yu [Comm. Math.
Phys., 334(30), 2015, pp. 1455--1482], and obtain an estimate on the
box-counting dimension of the singular set $S$, $d_B(S\cap \{t\geq t_0 \} )\leq
\frac13 (15-2s-8s^2) $ for every $t_0>0$.
